Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.

Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.

Cohesin-mediated loop anchors confine the locations of human replication origins.

DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability1,2. At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs)3-6, subTADs7 and loops8 in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase.

A Scientist's Oath.

Data on the perceptions of scientists suggest a moderate public distrust of scientist's motivations. Bettridge et al. suggest scientist's reluctance to engage the public on controversial ethical issues may be a contributing factor. The authors propose a Scientist's Oath to send a clear message to the public about our ideals.

Acoustic localization, validation, and characterization of Rice's whale calls.

The recently named Rice's whale in the Gulf of Mexico is one of the most endangered whales in the world, and improved knowledge of spatiotemporal occurrence patterns is needed to support their recovery and conservation. Passive acoustic monitoring methods for determining spatiotemporal occurrence patterns require identifying the species' call repertoire. Rice's whale call repertoire remains unvalidated though several potential call types have been identified. This study uses sonobuoys and passive acoustic tagging to validate the source of potential call types and to characterize Rice's whale calls. During concurrent visual and acoustic surveys, acoustic-directed approaches were conducted to obtain visual verifications of sources of localized sounds. Of 28 acoustic-directed approaches, 79% led to sightings of balaenopterid whales, of which 10 could be positively identified to species as Rice's whales. Long-moan calls, downsweep sequences, and tonal-sequences are attributed to Rice's whales based on these matches, while anthropogenic sources are ruled out. A potential new call type, the low-frequency downsweep sequence, is characterized from tagged Rice's whale recordings. The validation and characterization of the Rice's whale call repertoire provides foundational information needed to use passive acoustic monitoring for better understanding and conservation of these critically endangered whales.

Veterans' Preferences for Exchanging Information Using Veterans Affairs Health Information Technologies: Focus Group Results and Modeling Simulations.

BACKGROUND: The Department of Veterans Affairs (VA) has multiple health information technology (HIT) resources for veterans to support their health care management. These include a patient portal, VetLink Kiosks, mobile apps, and telehealth services. The veteran patient population has a variety of needs and preferences that can inform current VA HIT redesign efforts to meet consumer needs. OBJECTIVE: This study aimed to describe veterans' experiences using the current VA HIT and identify their vision for the future of an integrated VA HIT system. METHODS: Two rounds of focus group interviews were conducted with a single cohort of 47 veterans and one female caregiver recruited from Bedford, Massachusetts, and Tampa, Florida. Focus group interviews included simulation modeling activities and a self-administered survey. This study also used an expert panel group to provide data and input throughout the study process. High-fidelity, interactive simulations were created and used to facilitate collection of qualitative data. The simulations were developed based on system requirements, data collected through operational efforts, and participants' reported preferences for using VA HIT. Pairwise comparison activities of HIT resources were conducted with both focus groups and the expert panel. Rapid iterative content analysis was used to analyze qualitative data. Descriptive statistics summarized quantitative data. RESULTS: Data themes included (1) current use of VA HIT, (2) non-VA HIT use, and (3) preferences for future use of VA HIT. Data indicated that, although the Secure Messaging feature was often preferred, a full range of HIT options are needed. These data were then used to develop veteran-driven simulations that illustrate user needs and expectations when using a HIT system and services to access VA health care services. CONCLUSIONS: Patient participant redesign processes present critical opportunities for creating a human-centered design. Veterans value virtual health care options and prefer standardized, integrated, and synchronized user-friendly interface designs.

Double perovskite heterostructures: magnetism, Chern bands, and Chern insulators.

Experiments demonstrating the controlled growth of oxide heterostructures have raised the prospect of realizing topologically nontrivial states of correlated electrons in low dimensions. Here, we study heterostructures consisting of {111} bilayers of double perovskites separated by inert band insulators. In bulk, these double perovskites have well-defined local moments interacting with itinerant electrons leading to high temperature ferromagnetism. Incorporating spin-orbit coupling in the two-dimensional honeycomb geometry of a {111} bilayer, we find a rich phase diagram with tunable ferromagnetic order, topological Chern bands, and a C=±2 Chern insulator regime. Our results are of broad relevance to oxide materials such as Sr_{2}FeMoO_{6}, Ba_{2}FeReO_{6}, and Sr_{2}CrWO_{6}.

Observation of the Anomalous Hall Effect in a Layered Polar Semiconductor.

Progress in magnetoelectric materials is hindered by apparently contradictory requirements for time-reversal symmetry broken and polar ferroelectric electronic structure in common ferromagnets and antiferromagnets. Alternative routes can be provided by recent discoveries of a time-reversal symmetry breaking anomalous Hall effect (AHE) in noncollinear magnets and altermagnets, but hitherto reported bulk materials are not polar. Here, the authors report the observation of a spontaneous AHE in doped AgCrSe2 , a layered polar semiconductor with an antiferromagnetic coupling between Cr spins in adjacent layers. The anomalous Hall resistivity 3 µ Ω c m $\mu \Omega \, \textnormal {cm}$ is comparable to the largest observed in compensated magnetic systems to date, and is rapidly switched off when the angle of an applied magnetic field is rotated to ≈80° from the crystalline c-axis. The ionic gating experiments show that the anomalous Hall conductivity magnitude can be enhanced by modulating the p-type carrier density. They also present theoretical results that suggest the AHE is driven by Berry curvature due to noncollinear antiferromagnetic correlations among Cr spins, which are consistent with the previously suggested magnetic ordering in AgCrSe2 . The results open the possibility to study the interplay of magnetic and ferroelectric-like responses in this fascinating class of materials.

Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape.

Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen implicated disruption of kinase SMG1's phosphorylation of UPF1 as a potential disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro . Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases. One Sentence Summary: Disruption of the nonsense-mediated decay pathway with a newly developed SMG1 inhibitor with in-vivo activity increases the expression of T-cell targetable cancer neoantigens resulting from truncating mutations.

Review of a research report on postpartum depression impacted by home health visits.

The research findings from Tamaki's (2008) study are important to EBNP for both maternity and psychiatric-mental health nurses. Although the findings demonstrated that mental health visits showed improvement in women with postpartum depression, one suggestion would be to implement a study with a larger sample population and in multiple cultures. With support supplied by numerous quantitative and qualitative studies, such as Tamaki's (2008) study, postpartum depression could be treated with a new non-pharmaceutical measure that would be more beneficial and effective to women and their babies. It will also open new doors for EBNP in mental health and revolutionize home health nursing.

Topological skyrmion phases of matter.

We introduce topological phases of matter defined by skyrmions in the ground state spin---or pseudospin---expectation value textures in the Brillouin zone, the chiral and helical topological skyrmion phases of matter. These phases are protected by a symmetry present in centrosymmetric superconductors. We consider a tight-binding model for spin-triplet superconductivity in transition metal oxides and find it realizes each of these topological skyrmion phases. The chiral phase is furthermore realized for a parameter set characterizing Sr2RuO4 with spin-triplet superconductivity. We also find two types of topological phase transitions by which the skyrmion number can change. The second type occurs without the closing of energy gaps in a system described by a quadratic Hamiltonian without breaking the protecting symmetries when atomic spin-orbit coupling is non-negligible and there is a suitable additional degree of freedom. This contradicts the ``flat band'' limit assumption important in use of entanglement spectrum and Wilson loops, and in construction of the ten-fold way classification scheme of topological phases of matter. We furthermore predict two kinds of bulk-boundary correspondence signatures---one for measurements which execute a partial trace over degrees of freedom other than spin, which yields quantized transport signatures---and a second resulting from skyrmions trapping defects with their own non-trivial topology that is discussed in a second work, which yields generalizations of unpaired Majorana zero-modes.

Tissue cryopreservation using the 3M™ Novec™ 7000 freezing coolant offers a comparable and safe alternative to customary coolants.

Cryopreserving tissues for histology requires the use of coolants to buffer the sample from liquid nitrogen (LN2) and to control the rate of temperature decline. Several coolants sharing similar physical characteristics are available on the market; however, commonly used coolants are variably flammable and/or toxic and pose risks to personnel and facilities. The purpose of this study was to compare the performance of three commercially available coolants: hexane, 2-methylbutane (2 M), and 1-methoxyheptafluoropropane (N7000). Fresh mouse tissues were frozen by each method, for their ability to preserve microscopic architecture and to protect RNA from degradation were evaluated and compared to tissue characteristics obtained by direct immersion in LN2. Our results show that for most tissues, the N7000 freezing coolant provides equal or improved preservation of microscopic architecture. While snap-freezing tissues in LN2 provides superior RNA protection, no significant differences in RNA quality were seen between tissues frozen in hexane, 2 M, and N7000.

An isogenic cell line panel for sequence-based screening of targeted anticancer drugs.

We describe the creation of an isogenic cell line panel representing common cancer pathways, with features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cell lines were generated using CRISPR technologies. Surprisingly, most of these lines did not result in complete gene inactivation despite integration of sgRNA at the desired genomic site. A subset of the lines harbored biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterized lines covering 19 frequently lost cancer pathways. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of TP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena.

Steroid-induced fibroblast growth factors drive an epithelial-mesenchymal inflammatory axis in severe asthma.

Asthma and inflammatory airway diseases restrict airflow in the lung, compromising gas exchange and lung function. Inhaled corticosteroids (ICSs) can reduce inflammation, control symptoms, and improve lung function; however, a growing number of patients with severe asthma do not benefit from ICS. Using bronchial airway epithelial brushings from patients with severe asthma or primary human cells, we delineated a corticosteroid-driven fibroblast growth factor (FGF)-dependent inflammatory axis, with FGF-responsive fibroblasts promoting downstream granulocyte colony-stimulating factor (G-CSF) production, hyaluronan secretion, and neutrophilic inflammation. Allergen challenge studies in mice demonstrate that the ICS, fluticasone propionate, inhibited type 2-driven eosinophilia but induced a concomitant increase in FGFs, G-CSF, hyaluronan, and neutrophil infiltration. We developed a model of steroid-induced neutrophilic inflammation mediated, in part, by induction of an FGF-dependent epithelial-mesenchymal axis, which may explain why some individuals do not benefit from ICS. In further proof-of-concept experiments, we found that combination therapy with pan-FGF receptor inhibitors and corticosteroids prevented both eosinophilic and steroid-induced neutrophilic inflammation. Together, these results establish FGFs as therapeutic targets for severe asthma patients who do not benefit from ICS.

First Use of an Entire Age Cohort to Evaluate the Role of Sex in the Development of the Forensically Important Chrysomya megacephala (Diptera: Calliphoridae).

The age of a blow fly larval specimen found on a body can be used to estimate a minimum postmortem interval by comparing a physical feature of a larva (e.g., length) to a reference growth curve created under similar conditions. A better understanding of factors known to influence growth rates would lead to more precise estimates of larval age. A factor known to influence insect development, but almost always lacking in blow fly larval growth curves, is sex. We wanted to understand how sex might affect larval growth rates and therefore lead to more precise age estimates, in the forensically important blow fly Chrysomya megacephala (F.). We examined sex for an entire age cohort at 70 h and found on average, males were longer than females. To assess whether this difference would cause an investigator to interpret the results differently if comparing a larval specimen of one sex based on reference data from the other sex, we made sex-specific 95% prediction intervals. We did not find a difference when comparing a male specimen with the female prediction interval, but did find more females outside the interval than expected using the male interval. All females outside the male interval were shorter. Investigators commonly remove the largest individuals from a body to estimate age, so these females are less likely to be chosen. These results do not support the generation of sex-specific growth curves for this species, though this study's narrow scope means more information is required before making a final conclusion.

Higher-order topological insulators.

Three-dimensional topological (crystalline) insulators are materials with an insulating bulk but conducting surface states that are topologically protected by time-reversal (or spatial) symmetries. We extend the notion of three-dimensional topological insulators to systems that host no gapless surface states but exhibit topologically protected gapless hinge states. Their topological character is protected by spatiotemporal symmetries of which we present two cases: (i) Chiral higher-order topological insulators protected by the combination of time-reversal and a fourfold rotation symmetry. Their hinge states are chiral modes, and the bulk topology is Z2 -classified. (ii) Helical higher-order topological insulators protected by time-reversal and mirror symmetries. Their hinge states come in Kramers pairs, and the bulk topology is Z -classified. We provide the topological invariants for both cases. Furthermore, we show that SnTe as well as surface-modified Bi2TeI, BiSe, and BiTe are helical higher-order topological insulators and propose a realistic experimental setup to detect the hinge states.

Higher-Order Topology in Bismuth.

The mathematical field of topology has become a framework to describe the low-energy electronic structure of crystalline solids. A typical feature of a bulk insulating three-dimensional topological crystal are conducting two-dimensional surface states. This constitutes the topological bulk-boundary correspondence. Here, we establish that the electronic structure of bismuth, an element consistently described as bulk topologically trivial, is in fact topological and follows a generalized bulk-boundary correspondence of higher-order: not the surfaces of the crystal, but its hinges host topologically protected conducting modes. These hinge modes are protected against localization by time-reversal symmetry locally, and globally by the three-fold rotational symmetry and inversion symmetry of the bismuth crystal. We support our claim theoretically and experimentally. Our theoretical analysis is based on symmetry arguments, topological indices, first-principle calculations, and the recently introduced framework of topological quantum chemistry. We provide supporting evidence from two complementary experimental techniques. With scanning-tunneling spectroscopy, we probe the unique signatures of the rotational symmetry of the one-dimensional states located at step edges of the crystal surface. With Josephson interferometry, we demonstrate their universal topological contribution to the electronic transport. Our work establishes bismuth as a higher-order topological insulator.

Distribution of Abeta peptide in whole blood.

The measurement of amyloid beta peptides (Abeta) in blood and plasma is expected to be a useful biomarker as potential therapeutics designed to lower Abeta peptide enter clinical trials. Many reports have suggested that Abeta could bind to substances in blood that may influence the recovery of Abeta peptide in plasma, its detection by conventional ELISAs or the actual turnover and half-life of the peptide in blood. In this study we describe a process for analyzing total Abeta in whole blood and plasma using denaturing solid-phase extraction followed by reverse-phase HPLC linked to ELISA. Comparison of total Abeta peptide levels in whole blood and plasma from the same bleed showed that most of the Abeta peptide is captured in the plasma if the samples are first denatured. In contrast, plasma that was assayed without denaturation could show greater than 70% reduction in apparent total Abeta peptide. This suggested that there was a pool of Abeta peptide in non-denatured plasma that is occluded from detection by ELISA, perhaps by binding to plasma proteins.

Design principles for shift current photovoltaics.

While the basic principles of conventional solar cells are well understood, little attention has gone towards maximizing the efficiency of photovoltaic devices based on shift currents. By analysing effective models, here we outline simple design principles for the optimization of shift currents for frequencies near the band gap. Our method allows us to express the band edge shift current in terms of a few model parameters and to show it depends explicitly on wavefunctions in addition to standard band structure. We use our approach to identify two classes of shift current photovoltaics, ferroelectric polymer films and single-layer orthorhombic monochalcogenides such as GeS, which display the largest band edge responsivities reported so far. Moreover, exploring the parameter space of the tight-binding models that describe them we find photoresponsivities that can exceed 100 mA W-1. Our results illustrate the great potential of shift current photovoltaics to compete with conventional solar cells.

Genetic and non-genetic predictors of LINE-1 methylation in leukocyte DNA.

BACKGROUND: Altered DNA methylation has been associated with various diseases. OBJECTIVE: We evaluated the association between levels of methylation in leukocyte DNA at long interspersed nuclear element 1 (LINE-1) and genetic and non-genetic characteristics of 892 control participants from the Spanish Bladder Cancer/EPICURO study. METHODS: We determined LINE-1 methylation levels by pyrosequencing. Individual data included demographics, smoking status, nutrient intake, toenail concentrations of 12 trace elements, xenobiotic metabolism gene variants, and 515 polymorphisms among 24 genes in the one-carbon metabolism pathway. To assess the association between LINE-1 methylation levels (percentage of methylated cytosines) and potential determinants, we estimated beta coefficients (ßs) by robust linear regression. RESULTS: Women had lower levels of LINE-1 methylation than men (ß = -0.7, p = 0.02). Persons who smoked blond tobacco showed lower methylation than nonsmokers (ß = -0.7, p = 0.03). Arsenic toenail concentration was inversely associated with LINE-1 methylation (ß = -3.6, p = 0.003). By contrast, iron (ß = 0.002, p = 0.009) and nickel (ß = 0.02, p = 0.004) were positively associated with LINE-1 methylation. Single nucleotide polymorphisms (SNPs) in DNMT3A (rs7581217-per allele, ß = 0.3, p = 0.002), TCN2 (rs9606756-GG, ß = 1.9, p = 0.008; rs4820887-AA, ß = 4.0, p = 4.8 × 10-7; rs9621049-TT, ß = 4.2, p = 4.7 × 10-9), AS3MT (rs7085104-GG, ß = 0.7, p = 0.001), SLC19A1 (rs914238, TC vs. TT: ß = 0.5 and CC vs. TT: ß = -0.3, global p = 0.0007) and MTHFS (rs1380642, CT vs. CC: ß = 0.3 and TT vs. CC; ß = -0.8, global p = 0.05) were associated with LINE-1 methylation. CONCLUSIONS: We identified several characteristics, environmental factors, and common genetic variants that predicted DNA methylation among study participants.