The development of antiviral strategies requires a clear understanding of the principles that control the protein arrangements in viral shells. Considered here are those capsids that violate the paradigmatic Caspar and Klug (CK) model, and it is shown that the important structural features of such anomalous shells from the Picobirnaviridae, Flaviviridae and Leviviridae families can be revealed by models in the form of spherical icosahedral packings of equivalent rhombic structural units (SUs). These SUs are composed of protein dimers forming the investigated capsids which, as shown here, are based on the rhombic triacontahedron (RT) geometry. How to modify the original CK approach in order to make it compatible with the considered rhombic tessellations of a sphere is also discussed. Analogies between capsids self-assembled from dimers and trimers are demonstrated. This analysis reveals the principles controlling the localization of receptor proteins (which recognize the host cell) on the capsid surface.

An elementary method is described for finding the coordination sequences for a tiling, based on coloring the underlying graph. The first application is to the two kinds of vertices (tetravalent and trivalent) in the Cairo (or dual-32.4.3.4) tiling. The coordination sequence for a tetravalent vertex turns out, surprisingly, to be 1, 4, 8, 12, 16, …, the same as for a vertex in the familiar square (or 44) tiling. The authors thought that such a simple fact should have a simple proof, and this article is the result. The method is also used to obtain coordination sequences for the 32.4.3.4, 3.4.6.4, 4.82, 3.122 and 34.6 uniform tilings, and the snub-632 tiling. In several cases the results provide proofs for previously conjectured formulas.

The unit-cell reduction described by Selling and used by Delone (whose early publications were under the spelling Delaunay) is explained in a simple form. The transformations needed to implement the reduction are listed. The simplicity of this reduction contrasts with the complexity of Niggli reduction.

It is shown how to reconstruct the stacking sequence from the pairwise correlation functions between layers in close-packed structures. First, of theoretical interest, the analytical formulation and solution of the problem are presented when the exact pairwise correlation counts are known. In the second part, the practical problem is approached. A simulated annealing procedure is developed to solve the problem using as initial guess approximate solutions from previous treatments. The robustness of the procedure is tested with synthetic data, followed by an experimental example. The developed approach performs robustly over different synthetic and experimental data, comparing favorably with the reported methods.

Diffuse scattering is a rich source of information about disorder in crystalline materials, which can be modelled using atomistic techniques such as Monte Carlo and molecular dynamics simulations. Modern X-ray and neutron scattering instruments can rapidly measure large volumes of diffuse-scattering data. Unfortunately, current algorithms for atomistic diffuse-scattering calculations are too slow to model large data sets completely, because the fast Fourier transform (FFT) algorithm has long been considered unsuitable for such calculations [Butler & Welberry (1992). J. Appl. Cryst. 25, 391–399]. Here, a new approach is presented for ultrafast calculation of atomistic diffuse-scattering patterns. It is shown that the FFT can actually be used to perform such calculations rapidly, and that a fast method based on sampling theory can be used to reduce high-frequency noise in the calculations. These algorithms are benchmarked using realistic examples of compositional, magnetic and displacive disorder. They accelerate the calculations by a factor of at least 102, making refinement of atomistic models to large diffuse-scattering volumes practical.

When creating a System Composer architecture model, if the following functions are called with an invalid or missing stereotype, it can cause the model to get corrupted and might lead to a MATLAB crash:

• addComponent
• addPort
• connect

Simulink might produce an incorrect sorted order for a model that meets all of the following conditions:

• The model contains blocks from the SoC Blockset
• The Signal logging option is selected in the model configuration set
• Signals using asynchronous sample time are configured for logging

In the first reported crystal structure involving the potential ligand N,N',N''-tris(pyridin-2-yl)benzene-1,3,5-tricarboxamide, C24H18N6O3, intermolecular N—H...O hydrogen bonds link the molecules via their amide groups into slanted ladder-like chains, in which the uprights of the ladder are formed by the hydrogen-bonding interactions and the benzene ring cores of the molecules act as the rungs of the ladder. Only two of the three amide groups in the molecule are involved in hydrogen bonding and this influences the degree of out-of-plane twisting at each amide group, with the twist being more significant for those amide groups participating in hydrogen bonds.

An intuitive method is presented for detecting pseudosymmetries in Z' > 1 cases as a complement to well-proven strategies already available in the literature. It is based in the simple idea that the mid-points between equivalent atoms in symmetrically related mol­ecules are disposed according to simple well-known patterns, which are easily recognizable by optical inspection. A number of Z' = 4 cases in the literature are analyzed, which allows some of the potentialities of the method to be revealed.

The crystal structures of caesium di­hydrogen arsenate(V) bis­[tri­hydrogen arsen­ate(V)], Cs(H2AsO4)(H3AsO4)2, ammonium di­hydrogen arsenate(V) tri­hydrogen arsenate(V), NH4(H2AsO4)(H3AsO4), and dilithium bis­(di­hydrogen phosphate), Li2(H2PO4)2, were solved from single-crystal X-ray diffraction data. NH4(H2AsO4)(H3AsO4), which was hydro­thermally synthesized (T = 493 K), is homeotypic with Rb(H2AsO4)(H3AsO4), while Cs(H2AsO4)(H3AsO4)2 crystallizes in a novel structure type and Li2(H2PO4)2 represents a new polymorph of this composition. The Cs and Li compounds grew at room temperature from highly acidic aqueous solutions. Li2(H2PO4)2 forms a three-dimensional (3D) framework of PO4 tetra­hedra sharing corners with Li2O6 dimers built of edge-sharing LiO4 groups, which is reinforced by hydrogen bonds. The two arsenate compounds are characterized by a 3D network of AsO4 groups that are connected solely via multiple strong hydrogen bonds. A statistical evaluation of the As—O bond lengths in singly, doubly and triply protonated AsO4 groups gave average values of 1.70 (2) Å for 199 As—OH bonds, 1.728 (19) Å for As—OH bonds in HAsO4 groups, 1.714 (12) Å for As—OH bonds in H2AsO4 groups and 1.694 (16) Å for As—OH bonds in H3AsO4 groups, and a grand mean value of 1.667 (18) Å for As—O bonds to nonprotonated O atoms.

The title com­pound, tetra­ethyl­ammonium tetra­thio­rhenate, [(C2H5)4N][ReS4], has, at room temperature, a disordered structure in the space group P63mc (Z = 2, α-phase). A phase transition to the monoclinic space group P21 (Z = 2, γ-phase) at 285 K leads to a pseudo-merohedral twin. The high deviation from the hexa­gonal metric causes split reflections. However, the different orientations could not be separated, but were integrated using a large integration box. Rapid cooling to 110–170 K produces a metastable β-phase (P63, Z = 18) in addition to the γ-phase. All crystals of the β-phase are contaminated with the γ-phase. Additionally, the crystals of the β-phase are merohedrally twinned. In contrast to the α-phase, the β- and γ-phases do not show disorder.

An error in an equation in the paper by Song et al. [Acta Cryst. (2019), C75, 1353–1358] is corrected.

An operationally simple and time-efficient approach has been developed for the synthesis of racemic N-substituted 3-(2-aryl-2-oxoeth­yl)-3-hy­droxy­indolin-2-ones by a piperidine-catalysed aldol reaction between aryl methyl ketones and N-alkyl­isatins. These aldol products were used successfully as strategic inter­mediates for the preparation of N-substituted (E)-3-(2-hetaryl-2-oxo­ethyl­idene)indolin-2-ones by a stereoselective dehydration reaction under acidic conditions. The products have all been fully characterized by 1H and 13C NMR spectroscopy, by mass spectrometry and, for a representative selection, by crystal structure analysis. In each of (RS)-1-benzyl-3-hy­droxy-3-[2-(4-meth­oxy­phen­yl)-2-oxoeth­yl]indolin-2-one, C24H21NO4, (Ic), and (RS)-1-benzyl-3-{2-[4-(di­methyl­amino)­phen­yl]-2-oxoeth­yl}-3-hy­droxy­indolin-2-one, C25H24N2O3, (Id), inversion-related pairs of mol­ecules are linked by O—H⋯O hydrogen bonds to form R22(10) rings, which are further linked into chains of rings by a combination of C—H⋯O and C—H⋯π(arene) hydrogen bonds in (Ic) and by C—H⋯π(arene) hydrogen bonds in (Id). The mol­ecules of (RS)-1-benzyl-3-hy­droxy-3-[2-oxo-2-(pyridin-4-yl)eth­yl]indolin-2-one, C22H18N2O3, (Ie), are linked into a three-dimensional framework structure by a combination of O—H⋯N, C—H⋯O and C—H⋯π(arene) hydrogen bonds. (RS)-3-[2-(Benzo[d][1,3]dioxol-5-yl)-2-oxoeth­yl]-1-benzyl-3-hy­droxy­indolin-2-one, C24H19NO5, (If), crystallizes with Z' = 2 in the space group Poverline{1} and the mol­ecules are linked into com­plex sheets by a combination of O—H⋯O, C—H⋯O and C—H⋯π(arene) hydro­gen bonds. In each of (E)-1-benzyl-3-[2-(4-fluoro­phen­yl)-2-oxo­ethyl­idene]indolin-2-one, C23H16FNO2, (IIa), and (E)-1-benzyl-3-[2-oxo-2-(thiophen-2-yl)ethylidene]indolin-2-one, C21H15NO2S, (IIg), the mol­ecules are linked into simple chains by a single C—H⋯O hydrogen bond, while those of (E)-1-benzyl-3-[2-oxo-2-(pyridin-4-yl)ethyl­idene]indolin-2-one, C22H16N2O2, (IIe), are linked by three C—H⋯O hydrogen bonds to form sheets which are further linked into a three-dimensional structure by C—H⋯π(arene) hydrogen bonds. There are no hydrogen bonds in the structures of either (E)-1-benzyl-3-[2-(4-meth­oxy­phen­yl)-2-oxo­ethyl­idene]indolin-2-one, C24H19NO3, (IIc), or (E)-1-benzyl-5-chloro-3-[2-(4-chloro­phen­yl)-2-oxo­ethyl­idene]indolin-2-one, C23H15Cl2NO2, (IIh), but the mol­ecules of (IIh) are linked into chains of π-stacked dimers by a combination of C—Cl⋯π(arene) and aromatic π–π stacking inter­actions.

The positional change of nitro­gen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-de­aza­guanosine. Contrary to guanosine, this mol­ecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-de­aza­guanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4'-endo) for the ribose moiety, with an anti­periplanar orientation of the 5'-hy­droxy group. Crystal packing is controlled by inter­actions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2' of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H⋯O and N—H⋯O). The concept of pK-value differences to evaluate base-pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzo­furan to detect motional constraints by fluorescence spectroscopy.

A new polymorph (form II) is reported for the 1:1 dimethyl sulfoxide solvate of 2,3,5,6-tetra­fluoro-1,4-di­iodo­benzene (TFDIB·DMSO or C6F4I2·C2H6SO). The structure is similar to that of a previously reported polymorph (form I) [Britton (2003). Acta Cryst. E59, o1332–o1333], containing layers of TFDIB mol­ecules with DMSO mol­ecules between, accepting I⋯O halogen bonds from two TFDIB mol­ecules. Re-examination of form I over the temperature range 300–120 K shows that it undergoes a phase transformation around 220 K, where the DMSO mol­ecules undergo re-orientation and become ordered. The unit cell expands by ca 0.5 Å along the c axis and contracts by ca 1.0 Å along the a axis, and the space-group symmetry is reduced from Pnma to P212121. Refinement of form I against data collected at 220 K captures the (average) structure of the crystal prior to the phase transformation, with the DMSO mol­ecules showing four distinct disorder com­ponents, corresponding to an overlay of the 297 and 120 K structures. Assessment of the inter­molecular inter­action energies using the PIXEL method indicates that the various orientations of the DMSO mol­ecules have very similar total inter­action energies with the molecules of the TFDIB framework. The phase transformation is driven by inter­actions between DMSO mol­ecules, whereby re-orientation at lower temperature yields significantly closer and more stabilizing inter­actions between neighbouring DMSO mol­ecules, which lock in an ordered arrangement along the shortened a axis.

The backdrop of the stage with the Oscar Award is seen onstage during the 84th Academy Awards announcement held at the Academy of Motion Picture Arts and Sciences Samuel Goldwyn Theater on Jan. 24, 2012 in Los Angeles.; Credit: Kevin Winter/Getty Images

The Academy Awards have made history with breakthroughs for minorities in the past — but with this year's nominations, observers are noting how white the Oscars are, with no actors of color nominated in any of this year's acting categories.

It marks the least diverse nominations since 1998. People have been speaking out about this disconnect, with films like "Selma" being shut out of the acting nominations (though it did pick up a Best Picture nomination).

This content is from Southern California Public Radio. View the original story at SCPR.org.

The covers to the last issues of the current runs of "Avengers" and "New Avengers," leading into "Secret Wars."; Credit: Marvel

Marvel Comics held a press conference this week announcing details about "Secret Wars," a company-wide comic book crossover that they promise will change everything.

Promises of change in comics often don't amount to much, but here's why this one just might, with Marvel teasing that it will produce a whole new world for its characters.

"We see this as putting an endcap to decades of stories and starting a new era," said Marvel Editor-in-Chief Axel Alonso. "And when you see the scope of the event, you see what we're doing, what we're willing to do, this is a place where we're going to be bringing new pieces onto the board and taking old pieces off. You guys will be yelling and screaming, you'll be loving, hating, and in equal measure."

Reboot history

Rival DC Comics has always been quick to have stories designed to streamline their history, with the "Crisis on Infinite Earths" being the most famous one — a story that destroyed the DC Comics universe of the time, birthing a new timeline that gave us the versions of DC's heroes we know today. Several minor and major reboots followed, with the biggest since then being 2011's New 52 (and a tease of another one with this April's "Convergence").

Meanwhile, Marvel still refers back to stories from their early days, beginning with the first issue of "Marvel Comics" in 1939, and more so since the launch of "Fantastic Four" and the interlinked Marvel Universe in the 1960s, led by Stan Lee and Jack Kirby.

Marvel previously launched a line of comics meant to offer a fresh vision of the Marvel characters called Ultimate Comics, but now the worlds of those characters and the traditional Marvel universe are getting combined thanks to "Secret Wars."

"The Ultimate Universe, the Marvel Universe, they're going to smash together," said Alonso. "This is the Marvel Universe moving forward."

"We've never done anything like this, ever," said Marvel senior vice president and executive editor Tom Brevoort. "And what we're going to do to top it, I don't know. Hopefully that will be somebody else's problem."

The stories leading to "Secret Wars," and what is Battleworld?

The story that's been built up so far has to do with different universes colliding into each other — and in the first issue of "Secret Wars," the Marvel and Ultimate Earths collide, with the heroes of those worlds unable to stop it. What's left behind is what Marvel is calling "Battleworld," a patchwork planet with different parts of it inhabited by the characters from different famous Marvel crossovers of the past (you can see some of those past titles in the slideshow above).

Marvel released this video to help you visualize what exactly Battleworld is:

Battleworld video

See a map of Battleworld here, showing the different worlds made up of old storylines to be explored in "Secret Wars" (and click to enlarge):

Brevoort described Battleworld as "The little melting pot in which the new Marvel Universe will be created" after the Marvel and Ultimate versions of Earth are destroyed. He said that Battleworld is what Marvel is going to be "during, through and after" the beginning of "Secret Wars."

"Once you hit 'Secret Wars' 1, there is no Marvel Universe. There is no Ultimate Universe. All there is is Battleworld, and a whole lot of empty void," Brevoort said.

"Every single piece of this world is a building block for the Marvel Universe moving forward," Alonso said. "None of these stories are Elseworlds, or What Ifs, or alternative reality stories. They aren't set in the past or the future. They're not set in an alternate reality. They're set in the reality of the Marvel Universe."

It's also a story that uses an old name — the original "Secret Wars" involved an alien taking heroes from Earth and forcing them into battle for the fate of the universe. It remains unclear if the villain from that crossover will play a role here.

Why is Marvel rebooting?

Observers were quick to speculate on some of the behind-the-scenes reasons for the change. Combining the Ultimate Universe with the traditional Marvel Universe would let them incorporate the half-black, half-Latino Spider-Man from the Ultimate line that grabbed headlines a few years ago. It would let them do something different with characters like the X-Men and the Fantastic Four, who have been a flashpoint for controversy due to Fox retaining rights in perpetuity to any films based on those characters.

It also opens the door to a longtime comic book trope: Bringing back to life the dead.

"If we were to want to resurrect Gwen Stacy, this would be the place to do it, wouldn't it?" Alonso said.

What do creators and fans think about "Secret Wars"?

Speaking of the death of Gwen Stacy, the writer who pulled the trigger on killing her, Gerry Conway, tells Newsarama that he's on board.

"I think like with any idea, the execution will matter more than the idea itself. The idea of a reset is, by itself, not a bad idea," Conway said.

One who's less on board with it: longtime Spider-Man artist John Romita.

"My guess is new fans will be okay with it, and old fans will grumble," Romita told Newsarama. "I’m not a businessman, but I do know that comic companies, for almost 100 years now, do whatever they can for shock value. They grab attention. Personally, I hate all the goofy things they do. When I was there, I used to fight stuff like this. But you can’t stop them."

Current Marvel writers have been sworn to secrecy about what happens once "Secret Wars" is done:

Dan Slott tweet

The lack of certainty about what this all means has led fans to wildly speculate, as well as poke fun at what might happen:

Fan tweet 1

Fan tweet 2

It's a story that's been years in the making.

"Every single time we've done an event, we've always had to be mindful of 'Secret Wars,' and we've had to make decisions based on the fact that we knew that 'Secret Wars' was headed our way," Alonso said.

Brevoort said that Hickman proposed a version of "Secret Wars" years ago, but that vision has since become significantly larger.

"It sounds like typical Stan lee hyperbole — and there's nothing wrong with typical Stan Lee hyperbole — but it is difficult to imagine something that would be larger in scope, in scale, than what we are doing with 'Secret Wars,'" Brevoort said.

That father of the modern Marvel comics world, Stan Lee, tells Newsarama that the reboot is "probably good."

"Anything they do that’s unexpected and different usually captures the attention of the fans," Lee said. "It sounds intriguing to me."

Lee also tells Newsarama that if he were to do it all again, he'd do it basically the same, describing what he did as "the right way to go, and maybe sometimes, even the perfect way to go."

"I liked making the Fantastic Four superheroes without a secret identity. I liked the tragedy of Spider-Man’s origin, the ‘with great power, there must also come great responsibility.’ I thought it was the right way of doing things at the time. And I still like what I’ve done," Lee said. "I can’t think, off the top of my head, of anything I’d really want to change."

What does "Secret Wars" mean for fans?

More details are promised in the weeks to come, with a free preview issue being released on Free Comic Book Day, May 2. While fans wait, they may want to heed the wait-and-see approach advocated by Conway and famed "Thor" artist Walt Simonson.

"Maybe this is coming back out of my old geology days, but I try not to have instant reactions to things and say, ‘Oh my God! That’s terrible!’" Simonson told Newsarama. "My basic reaction is usually ‘let’s see the evidence in the field.’ Let’s come back in a year and see what we’ve got. That will tell the story.”

And for those who say that Marvel is ruining their childhood by messing with the history of their favorite characters, Conway tells Newsarama:

"I would say to them, no, your childhood is still your childhood. There’s a point to be made, and it’s a universal one: We have to see that there’s a difference between what people do today, and what they did yesterday. Yesterday still exists, those stories still exist. Now someone else is getting a chance at a new childhood. And that’s nice."

Watch the full "Secret Wars" live press conference below:

Secret Wars press conference video

This content is from Southern California Public Radio. View the original story at SCPR.org.

File: (L-R) "The Sarah Silverman Program" writer Harris Wittels, comedian Sarah Silverman, executive producer/head writer Dan Sterling and actress Laura Silverman, arrive at Comedy Central's Emmy Awards party at the STK restaurant Sept. 21, 2008 in Los Angeles.; Credit: Ethan Miller/Getty Images

Harris Wittels, a comedy writer who worked on "Parks & Recreation," has died at 30, the Los Angeles Police Department's Jane Kim tells KPCC.

Wittels was discovered by his assistant around 12 p.m., Kim said, and was already dead. Kim said that Wittels' death was a possible overdose, but that the Coroner's Office would determine the cause of death. Wittels had attended drug rehab twice.

Comedy Central, where Wittels worked on "The Sarah Silverman Program" and "Secret Girlfriend," confirmed Wittels' death, as did the comedy show he appeared at Wednesday night.

Comedy Central tweet

Meltdown Show tweet

Wittels was also well known for his @Humblebrag Twitter account and later book, helping to popularize the idea online of the false modesty of bragging while trying not to look like you're bragging.

Wittels had spoken about his struggles with addiction in places including Pete Holmes's podcast "You Made It Weird" in a November episode.

"I just really stopped caring about my life," Wittels said on "You Made It Weird," explaining how he got into doing drugs. "I just really started to think, well, if I'm only here for 80 years, then who cares if I spend it high or not?"

Wittels received his first big break when Sarah Silverman saw him performing comedy and gave him a job writing for her Comedy Central show.

Wittels also wrote for HBO's "Eastbound & Down," several MTV awards shows and the American Music Awards. He had a recurring role on "Parks & Recreation" and was a regular guest on the "Comedy Bang Bang" podcast.

Comedians, actors and fans mourned Wittels' death online.

Harris Wittels Storify

See Wittels in a scene from "Parks & Recreation":

Wittels on Parks & Recreation

Listen to Wittels on "Comedy Bang Bang":

Wittels on Comedy Bang Bang

This story has been updated.

This content is from Southern California Public Radio. View the original story at SCPR.org.

Entangled embedded periodic nets and crystal frameworks are defined, along with their dimension type, homogeneity type, adjacency depth and periodic isotopy type.

Quaternion methods for obtaining solutions to the problem of finding global rotations that optimally align pairs of corresponding lists of 3D spatial and/or orientation data are critically studied. The existence of multiple literatures and historical contexts is pointed out, and the algebraic solutions of the quaternion approach to the classic 3D spatial problem are emphasized. The treatment is extended to novel quaternion-based solutions to the alignment problems for 4D translation and orientation data.

A Landau theory for the wurtzite-based heterovalent ternary semiconductor ZnSnN2 is developed and a first-order reconstructive phase transition is proposed as the cause of observed crystal structure disorder. The model infers that the phase transition is paraelectric to antiferroelectric.

The analytical solution of the problem of X-ray spherical-wave Laue diffraction in a single crystal with a linear change of thickness on the exit surface is derived. General equations are applied to a specific case of plane-wave Laue diffraction in a thick crystal under the conditions of the Borrmann effect.

(The Paypers) Yoti has revealed a pair of partnerships to provide solutions combining its biometric technology...

(The Paypers) Fenergo, a provider of digital Client Lifecycle Management (CLM) software solutions for...