bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical and Socioeconomic Differences in Methamphetamine-Positive Burn Patients
Authors: Solomon Eve A , Greenhalgh David G , Sen Soman , Palmieri Tina L , Romanowski Kathleen S
Published: July 2019

Previous research on burn patients who test positive for methamphetamines (meth) has yielded mixed results regarding whether meth-positive status leads to worse outcomes and longer hospitalizations. We hypothesized that meth-positive patients at our regional burn center would have worse outcomes. We reviewed burn admissions from January 2014 to December 2017 and compared total patients versus meth-positive, and matched meth-negative versus meth-positive for total BSA burn, length of stay (LOS), intensive care unit (ICU) days, days on ventilator, discharge status (lived/died), number of operating room (OR) visits, number of procedures, socioeconomic status, comorbidities, and discharge disposition. Of 1363 total patients, 264 (19.4%) were meth-positive on toxicology screen. We matched 193 meth-positive patients with meth-negative controls based on TBSA burn, age, and inhalation injury. In the total population comparison, meth-positive patients had larger burns (15.6% vs 12.2%; P = .004), longer LOS (17.8 vs 14.3 days; P = .041), and fewer operations/TBSA (0.12 vs 0.2; P = .04), and lower socioeconomic status. Meth-positive patients were less likely to be discharged to a skilled nursing facility, and more likely to leave against medical advice. In the matched patients, we found no significant differences in LOS or OR visits/TBSA burn. Meth-positive patients have lower socioeconomic status, larger burns, and longer LOS compared to the total burn population. Methamphetamine use, by itself, does not appear to change outcomes. Methamphetamine use leads to larger burns in a population with fewer resources than the general population.
Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications
Authors: Han Cai , Sun Lin-Yu , Wang Wen-Tao , Sun Yu-Meng , Chen Yue-Qin
Published: July 2019

Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.
Forced Relocations: The Punitive Use of Mobility in Australia’s Immigration-detention Network
Authors: Peterie Michelle
Published: July 2019

In the interdisciplinary scholarship regarding immigration detention, the social, political and psychological costs of confinement are well documented. In recent years, however, scholars have also drawn attention to coerced forms of movement in some detention systems. Drawing on thirty in-depth, semi-structured interviews with volunteer visitors to Australia’s immigration-detention facilities, this article makes two main contributions to this scholarship. First, it presents empirical evidence regarding the use of forced mobility in Australia’s detention system. Dialoguing with work from other countries, it shows how these practices impact detainees and their supporters in the Australian context. Second, it builds upon and extends existing theoretical insights regarding the purposes of such mobility. While previous studies have concluded that relocations serve to isolate, punish and disorient prisoners, this article takes this argument a step further, positing that coerced mobility is also employed to encourage so-called ‘voluntary’ repatriations, thus serving overarching political objectives.
Shock fronts in the long GRB031203 host galaxy
Authors: Contini M
Published: July 2019

The detailed modelling of the spectra observed from the long GRB031203 host galaxy at different epochs during the 2003–2009 yr is presented. The line profiles show FWHM of ∼100 $\rm km\, s^{-1}$. A broad-line profile with FWHM ≤ 400 $\rm km\, s^{-1}$ appears in the line sockets from the 2009 observations. We suggest that the narrow lines show the velocity of starburst (SB) debris, while the broad ones are due to the wind from SB stars. The spectra are emitted from the gas downstream of different shock fronts which are at work on the edges of the emitting clouds. A head-on-back shock appears when the wind from the SB stars reaches the internal edge of the SB debris moving outwards. A head-on shock is created by collision of the debris with the ISM clouds. Line ratios in both cases are calculated by the coupled effect of shock and photoionization from the SB. The models selected by fitting the calculated to the observed line ratios show that the ionization parameters, the shock velocities and the gas pre-shock densities slowly decrease with time. Oxygen metallicities (12+log(O/H) = 8.3–8.48) are lower than solar (8.82) by a factor <3 and nitrogen metallicities are lower than solar (12 + log(N/H)  = 8.0, Grevesse & Sauval) by factors of 3–5.
COMPARISON OF THE RADIO-ISOTOPIC COMPOSITION BETWEEN HOT SPRING WATER OF HAMMAM DEBAGH AND ITS ASSOCIATED DEPOSITS
Authors: Boukhenfouf Wassila , Boucenna Ahmed
Published: July 2019

A radiological analysis of hot spring water of Hammam Debagh (also called Hammam Meskhoutine) and its associated deposits was realized. Hammam Debagh is considered to be the second hottest springs in the world with a temperature of 98°C and this lead to the creation of travertine. This later was formed because of limestone deposited by mineral springs in a rapid sedimentation of calcium, magnesium bicarbonates, and sulphides. The analysis showed that two-thirds of radioactivity was left by spring water in their deposits. The presence of uranium in the spring deposits was due to the property of the uranyl ion to form stable complexes with carbonates and precipitates. The radiation hazards indexes were estimated and compared with those given in literature.
Pathways to Modes of Movement Participation: Micromobilization in the Nashville Civil Rights Movement
Authors: Isaac Larry W , Coley Jonathan S , Cornfield Daniel B , Dickerson Dennis C
Published: July 2019

We employ a unique sample of participants in the early 1960s Nashville civil rights movement to examine within-movement micromobilization processes. Rather than assuming movement micromobilization and participation is internally homogeneous, we extend the literature by identifying distinct types of pathways (entry and preparation) and distinct types (or modes) of movement participation. Pathways into the Nashville movement are largely structured a priori by race, by several distinct points of entry (politically pulled, directly recruited, or professionally pushed), and by prior experience or training in nonviolent direct action. Participation falls into a distinct division of movement labor characterized by several major modes of participation—core cadre, soldiers, and supporters. We demonstrate that pathways and modes of participation are systematically linked and that qualitatively distinct pathways contribute to understanding qualitative modes of movement participation. Specifically, all core cadre members were pulled into activism, soldiers were either pulled or recruited, and supporters were pulled, recruited, or pushed. Highly organized, disciplined, and intense workshop training proved to be integral in becoming a member of the core cadre but not for soldier or supporter roles. We conclude that social movement studies would do well to pay more attention to variability in structured pathways to, preparation for, and qualitative dimensions of movement participation. These dimensions are critical to further understanding the way movements and their participants move and add insights regarding an important chapter in the southern civil rights movement. The implications of our findings extend to modes of movement activism more generally.
Post-discharge Acute Care and Outcomes in the Era of Readmission Reduction
Authors: Khera Rohan , Wang Yongfei , Bernheim Susannah M. , Lin Zhenqiu , Krumholz Harlan M.
Published: July 2019

Background

With incentives to reduce readmission rates, there are concerns that patients who need hospitalization after a recent hospital discharge may be denied access, which would increase their risk of mortality.

Objective

We determined whether patients with hospitalizations for conditions covered by national readmission programs who received care in emergency department (ED) or observation units but were not hospitalized within 30 days had an increased risk of death. We also evaluated temporal trends in post-discharge acute care utilization in inpatient units, emergency department (ED) and observation units for these patients.

Design, Setting, and Participants

In this observational study, national Medicare claims data for 2008-2016, we identified patients ≥65 years hospitalized with heart failure (HF), acute myocardial infarction (AMI), or pneumonia, conditions included in the HRRP.

Main Outcomes and Measures

Post-discharge 30-day mortality according to patients’ 30-day acute care utilization. Acute care utilization in inpatient and observation units, and the ED during the 30-day and 31-90-day post-discharge period.

Results

There were 3,772,924 hospitalizations for HF, 1,570,113 for AMI, and 3,131,162 for pneumonia. The overall post-discharge 30-day mortality was 8.7% for HF, 7.3% for AMI, and 8.4% for pneumonia. Post-discharge mortality increased annually by 0.16% (95% CI, 0.11%, 0.22%) for HF, decreased by 0.15% (95% CI, -0.18%, -0.12%) for AMI, and did not significantly change for pneumonia. Specifically, mortality only increased for HF patients who did not utilize any post-discharge acute care, increasing at a rate of 0.16% per year (95% CI, 0.11%, 0.22%), accounting for 99% of the increase in post-discharge mortality in heart failure. Concurrent with a reduction in 30-day readmission rates, 30-day observation stays and visits to the ED increased across all 3 conditions during and beyond the post-discharge 30-day period. There was no significant change in overall 30-day post-acute care utilization (P-trend >0.05 for all).

Conclusions and Relevance

The only condition with an increasing mortality through the study period was HF; the increase preceded the policy and was not present among those received ED or observation unit care without hospitalization. Overall, during this period, there was not a significant change in the overall 30-day post-discharge acute care utilization.
The sharedneoantigen landscape of MSI cancers reflects immunoediting during tumor evolution
Authors: Ballhausen Alexej , Przybilla Moritz Jakob , Jendrusch Michael , Haupt Saskia , Pfaffendorf Elisabeth , Draxlbauer Markus , Seidler Florian , Krausert Sonja , Ahadova Aysel , Kalteis Martin Simon , Heid Daniel , Gebert Johannes , Bonsack Maria , Schott Sarah , Bläker Hendrik , Seppälä Toni , Mecklin Jukka-Pekka , Broeke Sanne Ten , Nielsen Maartje , Heuveline Vincent , Krzykalla Julia , Benner Axel , Riemer Angelika Beate , von Knebel Doeberitz Magnus , Kloor Matthias
Published: July 2019

The immune system can recognize and attack cancer cells, especially those with a high load of mutation-inducedneoantigens. Suchneoantigens are particularly abundant in DNA mismatch repair (MMR)-deficient, microsatellite-unstable (MSI) cancers. MMR deficiency leads to insertion/deletion (indel) mutations at coding microsatellites (cMS) and toneoantigen-inducing translational frameshifts. The abundance of mutationalneoantigens renders MSI cancers sensitive to immune checkpoint blockade. However, the neoantigen landscape of MMR-deficient cancers has not yet been systematically mapped. In the present study, we used a novel tool to monitorneoantigen-inducing indel mutations in MSI colorectal and endometrial cancer. Our results show that MSI cancers share several highly immunogenicneoantigens that result from specific, recurrent indel mutation events. Notably, the frequency of such indel mutations was negatively correlated to the predicted immunogenicity of the resultingneoantigens. These observations suggest continuous immunoediting of emerging MMR-deficient cells during tumor evolution.

One sentence summary

Quantitative indel mutation analysis reveals evidence of immune selection in mismatch repair-deficient cancers
Genomic re-assessment of the transposable element landscape of the potato genome
Authors: Zavallo Diego , Crescente Juan Manuel , Gantuz Magdalena , Leone Melisa , Vanzetti Leonardo Sebastian , Masuelli Ricardo Williams , Asurmendi Sebastian
Published: July 2019

Transposable elements (TEs) are DNA sequences with the ability to auto-replicate and move throughout the host genome. TEs are major drivers in stress response and genome evolution. Given their significance, the development of clear and efficient TE annotation pipelines has become essential for many species. The latest de novo TE discovery tools, along with available TEs from Repbase and sRNA-seq data, allowed us to perform a reliable potato TEs detection, classification and annotation through an open-source and freely available pipeline (https://github.com/DiegoZavallo/TE_Discovery). Using a variety of tools, approaches and rules, our pipeline revealed that ca. 16% of the potato genome can be clearly annotated as TEs. Additionally, we described the distribution of the different types of TEs across the genome, where LTRs and MITEs present a clear clustering pattern in pericentromeric and subtelomeric/telomeric regions respectively. Finally, we analyzed the insertion age and distribution of LTR retrotransposon families which display a distinct pattern between the two major superfamilies. While older Gypsy elements concentrated around heterochromatic regions, younger Copia elements located predominantly on euchromatic regions. Overall, we delivered not only a reliable, ready-to-use potato TE annotation files, but also all the necessary steps to perform de novo detection for other species.

Key Message

We provide a comprehensive and reliable potato TE landscape, based on a wide variety of identification tools and integrative approaches, producing clear and ready-to-use outputs for the scientific community.
Impaired early visual categorization of fear in social anxiety
Authors: Meynadasy Melissa , Clancy Kevin , Simon Jessica , Wu Wei , Li Wen
Published: July 2019

Social anxiety is associated with biased social perception, especially of ambiguous cues. While aberrations in high-level processes, including cognitive appraisal and interpretation of social signals, have been implicated in such biases, contributions of early, low-level stimulus processing remain unclear. Categorical perception is known to be an efficient process to resolve signal ambiguity, and categorical emotion perception can swiftly classify sensory input, “tagging” biologically important stimuli at early stages of processing to facilitate ecological response. However, early threat categorization could be disrupted by exaggerated threat processing in anxiety, resulting in biased perception of ambiguous signals. We tested this hypothesis among individuals with low and high trait social anxiety (LSA and HSA), who performed a 2-alternative-forced-choice (fear or neutral) task on facial expressions parametrically varied along a neutral-fear continuum. Clear divergence between the groups emerged in the profiles of reaction time (RT) and early visual response along the neutral-fear continuum. The LSA group exhibited a RT profile characteristic of categorical perception with drastically increased RT from neutral to intermediate (boundary) fear intensities, contrasting monotonous, non-significant RT changes in the HSA group. Neurometric analysis along the continuum identified an early fear-neutral categorization operation (arising in the P1, an early visual event-related potential/ERP at 100 ms) in the LSA (but not HSA) group. Absent group differences in higher-level cognitive operations (identified by later ERPs), current findings highlight a dispositional cognitive vulnerability in early visual categorization of social threat, which could precipitate further cognitive aberrations and, eventually, the onset of social anxiety disorder.
Blocking neuroestrogen synthesis modifies neural representations of learned song without altering vocal imitation accuracy in developing songbirds
Authors: Vahaba Daniel M. , Hecsh Amelia , Remage-Healey Luke
Published: July 2019

Birdsong, like human speech, is learned early in life by first memorizing an auditory model. Once memorized, birds compare their own burgeoning vocalizations to their auditory memory, and adjust their song to match the model. While much is known about this latter part of vocal learning, less is known about how initial auditory experiences are formed and consolidated. In both adults and developing songbirds, there is strong evidence suggesting the caudomedial nidopallium (NCM), a higher order auditory forebrain area, is the site of auditory memory consolidation. However, the mechanisms that facilitate this consolidation are poorly understood. One likely mechanism is 17β-estradiol (E2), which is associated with speech-language development and disorders in humans, and is abundant in both mammalian temporal cortex and songbird NCM. Circulating E2 is also elevated during the auditory memory phase, and in NCM immediately after song learning sessions, suggesting it functions to encode recent auditory experience. Therefore, we tested a role for E2 production in auditory memory consolidation during development using a comprehensive set of investigations to ask this question at the level of neuroanatomy, neurophysiology, and behavior. Our results demonstrate that while systemic estrogen synthesis blockade regulates juvenile song production, inhibiting E2 synthesis locally within NCM does not adversely affect song learning outcomes. Surprisingly, early life E2 manipulations in NCM modify the neural representations of birds’ own song and the model tutor song in both NCM and a downstream sensorimotor nucleus (HVC). Further, we show that the capacity to synthesize neuroestrogens remains high throughout development alongside substantial changes in NCM cell density across age. Taken together, these findings suggest that E2 plays a multifaceted role during development, and demonstrate that contrary to prediction, unilateral post-training estrogen synthesis blockade in the auditory cortex does not negatively impact vocal learning. Acute downregulation of neuroestrogens are therefore likely permissive for juvenile auditory memorization, while neuroestrogen synthesis influences communication production and representation in adulthood.
ChassiDex: A microbial database useful for synthetic biology applications
Authors: Kailash B P , Karthik D , Shinde Mousami , Damaraju Nikhita , Muthukrishnan Anantha Barathi , Prasad Shashi Bala , Jayaraman Guhan
Published: July 2019

ChassiDex is an open-source, non-profit online host organism database that houses a repository of molecular, biological and genetic data for model organisms with applications in synthetic biology. The structured user-friendly environment makes it easy to browse information. The database consists of a page for each model organism subdivided into sections such as Growth Characteristics, Strain diversity, Culture sources, Maintenance protocol, Transformation protocol, BioBrick parts and commonly used vectors. With tools such as CUTE built for codon usage table generator, it is also easy to generate and download accurate novel codon tables for unconventional hosts in suitable formats. This database was built as a project for the International Genetically Engineered Machine Competition in 2017 with the mission of making it easy to shift from working with one host organism to another unconventional host organism for any researcher in the field of synthetic biology. The code along with other instructions for the usage of the database and tools are publicly available at the GitHub page. We encourage the synthetic biology community to contribute to the database by adding data for any additional or existing host organism.

https://chassidex.org;https://github.com/ChassiDex
Evolution of barrier loci at an intermediate stage of speciation with gene flow
Authors: Liu Xiaodong , Glémin Sylvain , Karrenberg Sophie
Published: July 2019

Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of differentiation; however, the underlying mechanisms are not well understood. We used an integrated approach to investigate evolutionary processes governing genetic differentiation between the hybridizing campions (Silene dioica (L.) Clairv. and S. latifolia Poiret). Demographic modeling indicated that the two species diverged with continuous gene flow. The best-supported scenario with heterogeneity in both migration rate and effective population size suggested that 5% of the loci evolved without gene flow. Differentiation (FST) and sequence divergence (dXY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection and differentiation was significantly elevated around previously identified QTLs associated with assortative mating. In between-species population pairs, isolation by distance was stronger for genomic regions with low between-species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated suggesting that the interplay of background selection and conserved genomic features is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection drove the evolution of barrier loci played and the genomic landscape of differentiation between the two species, consistent with predictions for speciation in the face of gene flow.
Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data
Authors: Bhati Meenu , Kadri Naveen Kumar , Crysnanto Danang , Pausch Hubert
Published: July 2019

Background

Autochthonous cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution.

Results

We annotated 15,722,811 million SNPs and 1,580,878 million Indels including 10,738 and 2,763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10-3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding quantified using runs of homozygosity (ROH) was relatively low (FROH=0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in more recent generations of OB cattle (FROH=0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P< 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus.

Conclusions

We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation and adoption of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.
Testing for population decline using maximal linkage disequilibrium blocks
Authors: Kerdoncuff Elise , Lambert Amaury , Achaz Guillaume
Published: July 2019

Only 6% of known species have a conservation status. Methods that assess conservation statuses are often based on individual counts and are thus too laborious to be generalized to all species. Population genomics methods that infer past variations in population size are easy to use but limited to the relatively distant past. Here we propose a population genomics approach that tests for recent population decline and may be used to assess species conservation statuses. More specifically, we study Maximal Recombination Free (MRF) blocks, that are segments of a sequence alignment inherited from a common ancestor without recombination. MRF blocks are relatively longer in small than in large populations. We use the distribution of MRF block lengths rescaled by their mean to test for recent population decline. However, because MRF blocks are difficult to detect, we also consider Maximal Linkage Disequilibrium (MLD) blocks, which are runs of single nucleotide polymorphisms compatible with a single tree. We develop a new method capable of inferring a very recent decline (e.g. with a detection power of 50% for populations which size was halved toN, 0.05 ×Ngenerations ago) from rescaled MLD block lengths. Our framework could serve as a basis for quantitative tools to assess conservation status in a wide range of species.
Predicting protein functional motions: an old recipe with a new twist
Authors: Grudinin Sergei , Laine Elodie , Hoffmann Alexandre
Published: July 2019

Large macromolecules, including proteins and their complexes, very often adopt multiple conformations. Some of them can be seen experimentally, for example with X-ray crystallography or cryo-electron microscopy. This structural heterogeneity is not occasional and is frequently linked with specific biological function. Thus, the accurate description of macromolecular conformational transitions is crucial for understanding fundamental mechanisms of life’s machinery. We report on a real-time method to predict such transitions by extrapolating from instantaneous eigen-motions, computed using the normal mode analysis, to a series of twists. We demonstrate the applicability of our approach to the prediction of a wide range of motions, including large collective opening-closing transitions and conformational changes induced by partner binding. We also highlight particularly difficult cases of very small transitions between crystal and solution structures. Our method guaranties preservation of the protein structure during the transition and allows to access conformations that are unreachable with classical normal mode analysis. We provide practical solutions to describe localized motions with a few low-frequency modes and to relax some geometrical constraints along the predicted transitions. This work opens the way to the systematic description of protein motions, whatever their degree of collectivity. Our method is available as a part of the NOn-Linear rigid Block (NOLB) package athttps://team.inria.fr/nano-d/software/nolb-normal-modes/.

Significance Statement

Proteins perform their biological functions by changing their shapes and interacting with each other. Getting access to these motions is challenging. In this work, we present a method that generatesplausiblephysics-based protein motions and conformations. We model a protein as a network of atoms connected by springs and deform it along the least-energy directions. Our main contribution is to perform the deformations in a nonlinear way, through a series of twists. This allows us to produce a wide range of motions, some of them previously inaccessible, and to preserve the structure of the protein during the motion. We are able to simulate the opening or closing of a protein and the changes it undergoes to adapt to a partner.
A new species of Lepanthopsis (Orchidaceae, Pleurothallidinae) in the Atlantic Forest in São Paulo, Brazil
Authors: Zandoná L.R. , Catharino E.L.M. , Maragni A.G. , Jesus M.M.F.
Published: July 2019

A new species of Lepanthopsis is discovered and described for the Atlantic Forest of southeastern Brazil, the species called Lepanthopsis legadensis is distinguished from other Brazilian species, notably by the petals and long-acuminate sepals.
Myosoft: an automated muscle histology analysis tool using machine learning algorithm utilizing FIJI/ImageJ software
Authors: Encarnacion-Rivera Lucas , Foltz Steven , Hartzell H. Criss , Choo Hyo-Jung
Published: July 2019

Background

Skeletal muscle is comprised of a heterogeneous population of muscle fibers which can be classified by their metabolic and contractile properties (fiber “types”). Fiber type is a primary determinant of muscle function along with fiber size (cross-sectional area). The fiber type composition of a muscle responds to physiological changes like exercise and aging and is often altered in disease states. Thus, analysis of fiber size and type in histological muscle preparations is a useful method for quantifying key indicators of muscle function and for measuring responses to a variety of stimuli or stressors. These analyses are near-ubiquitous in the fields of muscle physiology and myopathy, but are most commonly performed manually, which is highly labor- and time-intensive. To offset this obstacle, we developed Myosoft, a novel method to automate morphometric and fiber type analysis in muscle sections stained with fluorescent antibodies.

Methods

Muscle sections were stained for cell membrane (laminin) and myofiber type (myosin heavy chain isoforms). Myosoft, running in the open access software platform FIJI (ImageJ), was used to analyze myofiber size and type in transverse sections of entire gastrocnemius/soleus muscles.

Results

Myosoft provides accurate analysis of muscle histology >50-times faster than manual analysis. We demonstrate that Myosoft is capable of handling high-content images even when image or staining quality is suboptimal, which is a marked improvement over currently available, comparable programs.

Conclusions

Myosoft is a reliable, accurate, high-throughput, and convenient tool to analyze high-content muscle histology. Myosoft is freely available to download from Github athttps://github.com/Hyojung-Choo/Myosoft/tree/Myosoft-hub.
Huntingtin fibrils with different toxicity, structure, and seeding potential can be reversibly interconverted
Authors: Isas J. Mario , Pandey Nitin K. , Teranishi Kazuki , Okada Alan K. , Applebaum Anise , Meier Franziska , Langen Ralf , Siemer Ansgar B.
Published: July 2019

The first exon of the huntingtin protein (HTTex1) important in Huntington’s Disease (HD) can form cross-β fibrils of varying toxicity. We find that the difference between these fibrils is the degree of entanglement and dynamics of the C-terminal proline-rich domain (PRD) in a mechanism analogous to polyproline film formation. In contrast to fibril strains found for other cross-β fibrils, these HTTex1 fibril types can be reversibly interconverted. This is because the structure of their polyQ fibril core remains unchanged. Further, we find that more toxic fibrils of low entanglement have higher affinities for protein interactors and are more effective seeds for recombinant HTTex1 and HTTex1 in cells. Together these data show how the structure of a framing sequence at the surface of a fibril can modulate seeding, protein-protein interactions, and thereby toxicity in neurodegenerative disease.
ASCL1-regulated DARPP-32 and t-DARPP stimulate small cell lung cancer growth and neuroendocrine tumor cell survival
Authors: Alam Sk. Kayum , Wang Li , Ren Yanan , Hernandez Christina E. , Kosari Farhad , Roden Anja C. , Yang Rendong , Hoeppner Luke H.
Published: July 2019

Small cell lung cancer (SCLC) is the most aggressive form of lung cancer, and new molecular insights are necessary for prognostic and therapeutic advances. Here we demonstrate in orthotopic mouse models that dopamine and cAMP-regulated phosphoprotein, Mr 32000 (DARPP-32) and its N-terminally truncated splice variant t-DARPP promote SCLC growth through increased proliferation, Akt/Erk-mediated survival and anti-apoptotic signaling. DARPP-32 and t-DARPP proteins are overexpressed in SCLC patient-derived tumor tissue, but virtually undetectable in physiologically normal lung. RNA sequencing analysis reveals a subset of SCLC patients with high tumoral t-DARPP expression and upregulated Notch signaling genes, including achaete-scute homologue 1 (ASCL1). We show that DARPP-32 isoforms are transcriptionally activated by ASCL1 in human SCLC cells. Taken together, we demonstrate new regulatory mechanisms of SCLC oncogenesis that suggest DARPP-32 isoforms may represent a negative prognostic indicator for SCLC and serve as a potential target for the development of new therapies.
Diffusion analysis of single particle trajectories in a Bayesian nonparametrics framework
Authors: Falcao Rebeca Cardim , Coombs Daniel
Published: July 2019

Single particle tracking (SPT), where individual molecules are fluorescently labelled and followed over time, is an important tool that allows the spatiotemporal dynamics of subcellular biological systems to be studied at very fine temporal and spatial resolution. Mathematical models of particle motion are typically based on Brownian diffusion, reflecting the noisy environment that biomolecules typically inhabit. In order to study changes in particle behaviour within individual tracks, Hidden Markov models (HMM) featuring multiple diffusive states have been used as a descriptive tool for SPT data. However, such models are typically specified with an a-priori defined number of particle states and it has not been clear how such assumptions have affected their outcomes. Here, we propose a method for simultaneously inferring the number of diffusive states alongside the dynamic parameters governing particle motion. Our method is an infinite HMM (iHMM) within the general framework of Bayesian non-parametric models. We directly extend previous applications of these concepts in molecular biophysics to the SPT framework and propose and test an additional constraint with the goal of accelerating convergence and reducing computational time. We test our iHMM using simulated data and apply it to a previously-analyzed large SPT dataset for B cell receptor motion on the plasma membrane of B cells of the immune system.
Synaptotagmin-7 endows a population of chromaffin cell vesicles with enhanced calcium sensing and delayed content release properties
Authors: Bendahmane M , Kreutzberger AJB , Chapman-Morales A , Philippe J , Schenk N , Zhang S , Kiessling V , Tamm L , Giovannucci DR , Jenkins PM , Anantharam A
Published: July 2019

Synaptotagmin-7 (Syt-7) is one of two major calcium sensors for exocytosis in adrenal chromaffin cells, the other being synaptotagmin-1 (Syt-1). Despite its undoubted importance, questions remain as to the functional and physiological role of Syt-7 in secretion. We examined this issue using two distinct preparations - mouse chromaffin cells lacking endogenous Syt-7 (KO cells) and a reconstituted system employing cell-derived vesicles expressing either Syt-7 or Syt-1. First, we report using immunofluorescence that Syt-7 exhibits a punctate intracellular distribution consistent with its sorting to organelles, including dense core vesicles. We also find that the likelihood of vesicle fusion in KO cells is markedly lower than in WT cells. When fusion does occur, cargoes are discharged more rapidly when only Syt-1 is available to facilitate release. A distinctive characteristic of KO cells is that secretion runs down after prolonged cholinergic stimulation. In contrast, exocytosis persists in WT cells even with extended exposure to acetylcholine, suggesting a key role for Syt-7 in sustaining the secretory response. To determine the extent to which the aforementioned results are attributable purely to Syt-7, vesicles expressing only Syt-7 or Syt-1 were triggered to fuse on planar supported bilayers bearing plasma membrane SNARE proteins. Here, as in cells, Syt-7 confers substantially greater calcium sensitivity to vesicle fusion than Syt-1 and slows the rate at which cargos are released. Overall, this study demonstrates that by virtue of its high affinity for calcium, Syt-7 plays a central role in regulating secretory output from adrenal chromaffin cells.
The Ciliary Lumen Accommodates Passive Diffusion and Vesicle Trafficking in Cytoplasmic-Ciliary Transport
Authors: Ruba Andrew , Luo Wangxi , Yu Jingjie , Takao Daisuke , Evangelou Athanasios , Higgins Rachel , Khim Saovleak , Verhey Kristen J. , Yang Weidong
Published: July 2019

Transport of membrane and cytosolic proteins into the primary cilium is essential for its role in cellular signaling. Using single molecule microscopy, we mapped the movement of membrane and soluble proteins at the base of the primary cilium. In addition to the well-known intraflagellar transport (IFT) route, we identified two new pathways within the lumen of the primary cilium - passive diffusional and vesicle transport routes - that are adopted by proteins for cytoplasmic-cilium transport in live cells. Independent of the IFT path, approximately half of IFT motors (KIF3A) and cargo (α-tubulin) take the passive diffusion route and more than half of membrane-embedded G protein coupled receptors (SSTR3 and HTR6) use RAB8A-regulated vesicles to transport into and inside cilia. Furthermore, ciliary lumen transport is the preferred route for membrane proteins in the early stages of ciliogenesis and inhibition of SSTR3 vesicle transport completely blocks ciliogenesis. Furthermore, clathrin-mediated, signal-dependent internalization of SSTR3 also occurs through the ciliary lumen. These transport routes were also observed inChlamydomonas reinhardtiiflagella, suggesting their conserved roles in trafficking of ciliary proteins.
Instructor-learner brain coupling discriminates between instructional approaches and predicts learning
Authors: Pan Yafeng , Dikker Suzanne , Goldstein Pavel , Zhu Yi , Yang Cuirong , Hu Yi
Published: July 2019

The neural mechanisms that support naturalistic learning via effective pedagogical approaches remain elusive. Here we use functional near-infrared spectroscopy to measure brain activity from instructor-learner dyads simultaneously during dynamic conceptual learning. We report that brain-to-brain coupling is correlated with learning outcomes, and, crucially, appears to be driven by specific scaffolding behaviors on the part of the instructors (e.g., asking guiding questions or providing hints). Brain-to-brain coupling enhancement is absent when instructors use an explanation approach (e.g., providing definitions or clarifications). Finally, we find that machine-learning techniques are more successful when decoding instructional approaches (scaffolding vs. explanation) from brain-to-brain coupling data than when using a single-brain method. These findings suggest that brain-to-brain coupling as a pedagogically relevant measure tracks the naturalistic instructional process during instructor-learner interaction throughout constructive engagement, but not information clarification.
Single-cell sequencing reveals a clonal expansion of pro-inflammatory synovial CD8 T cells expressing tissue homing receptors in psoriatic arthritis
Authors: Penkava Frank , Del Castillo Velasco-Herrera Martin , Young Matthew D , Yager Nicole , Lara Alicia Lledo , Guzzo Charlotte , Maroof Ash , Mamanova Lira , Cole Suzanne , Efremova Mirjana , Simone Davide , Brown Chrysothemis C , Croxford Andrew L , Teichmann Sarah , Bowness Paul , Behjati Sam , Al-Mossawi M Hussein
Published: July 2019

Psoriatic arthritis (PsA) is a debilitating immune-mediated inflammatory arthritis of unknown pathogenesis commonly affecting patients with skin psoriasis. We used three complementary single cell approaches to study leukocytes from PsA joints. Mass cytometry (CyTOF) demonstrated marked (>3 fold) expansion of memory CD8 T cells in the joints compared to matched blood. Further exploration of the memory CD8 compartment using both droplet and plate based single cell RNA sequencing of paired alpha and beta chain T cell receptor sequences identified pronounced CD8 T cell clonal expansions within the joints, strongly suggesting antigen driven expansion. These clonotypes exhibited distinct gene expression profiles including cycling, activation, tissue homing and tissue residency markers. Pseudotime analysis of these clonal CD8 populations identified trajectories in which tissue residency can represent an intermediate developmental state giving rise to activated, cycling and exhausted CD8 populations. Comparing T-cell clonality across patients further revealed specificity convergence of clones against a putative common antigen. We identify chemokine receptor CXCR3 as upregulated in expanded synovial clones, and elevation of two CXCR3 ligands, CXCL9 and CXCL10, in PsA synovial fluid.
Tetrad analysis without tetrad dissection: Meiotic recombination and genomic diversity in the yeast Komagataella phaffii (Pichia pastoris)
Authors: Braun-Galleani Stephanie , Dias Julie A. , Coughlan Aisling Y. , Ryan Adam P. , Byrne Kevin P. , Wolfe Kenneth H.
Published: July 2019

Komagataella phaffii is a yeast widely used in the pharmaceutical and biotechnology industries, and is one of the two species that were formerly called Pichia pastoris. However, almost all laboratory work on K. phaffii has been done on strains derived from a single natural isolate, CBS7435. There is little information about the genetic properties of K. phaffii or its sequence diversity. Genetic analysis is difficult because, although K. phaffii makes asci with four spores, the spores are small and tend to clump together, making the asci hard to dissect. Here, we sequenced the genomes of all the known isolates of this species, and find that K. phaffii has only been isolated from nature four times. We analyzed the meiotic recombination landscape in a cross between auxotrophically marked strains derived from two isolates that differ at 44,000 single nucleotide polymorphism sites. We conducted tetrad analysis by making use of the property that haploids of this species do not mate in rich media, which enabled us to isolate and sequence the four types of haploid cell that are present in the colony that forms when a tetratype ascus germinates. We found that approximately 25 crossovers occur per meiosis, which is 3.5 times fewer than in Saccharomyces cerevisiae. Recombination is suppressed, and genetic diversity among natural isolates is low, in a region around centromeres that is much larger than the centromeres themselves. Our method of tetrad analysis without tetrad dissection will be applicable to other species whose spores do not mate spontaneously after germination.

Author summary

To better understand the basic genetics of the budding yeast Komagataella phaffii, which has many applications in biotechnology, we investigated its genetic diversity and its meiotic recombination landscape. We made a genetic cross between strains derived from two natural isolates, and developed a method for characterizing the genomes of the four spores resulting from meiosis, which were previously impossible to isolate. We found that K. phaffii has a lower recombination rate than Saccharomyces cerevisiae. It shows a large zone of suppressed recombination around its centromeres, which may be due to the structural differences between centromeres in K. phaffii and S. cerevisiae.
Biodiversity conservation in cities: Defining habitat analogs for plant species of conservation interest
Authors: Itani M , Al Zein M. , Nasralla N. , Talhouk S. N.
Published: July 2019

Urban plant habitats have become primary drivers of species interactions. They consist of managed vegetation and spontaneous assemblages of native, naturalized, ornamental garden escapes, and invasive species. Our objective was to define urban habitat analogs for a plant species of conservation interest,Matthiola crassifolia,which has persisted in varying abundance in the Mediterranean city of Beirut.

We adopted a stepwise method that integrates two vegetation assessments, floristics, and physiognomy. We placed seventy-eight quadrats (1m x 1m) in 12 study sites following a deliberate biased method to capture habitat diversity. In every quadrat, we performed taxonomic identification and recorded life form of each species. We pooled species that shared the same life form into categories and estimated area cover for each of these life forms. We performed TWINSPAN analysis on floristic data to identify species positively associated withM. crassifolia,and on life forms, to determine plant assemblages that promote optimalM. crassifoliarepresentation. We then combined findings from both analyses to generate a description of urban habitat analogs suitable forM. crassifolia.

The results revealed that urban habitat analogs favorable toM. crassifoliainclude green spaces dominated by palms, low-lying succulents, or by shrubs with scale-like leaves. On the other hand, spaces dominated by turf grass, canopy trees, or vegetation that produces significant litter were not favorable toM. crassifolia’s persistence. Based on these findings, we generated a plant palette of native and non-native species to design urban habitat analogs favorable to the persistence ofM. crassifolia.

Synthesis and applications

The application of this method can inform planting designs that yield suitable habitats for plants of conservation interest. It can also guide landscape management plans that seek to create or modify green spaces to optimize growing conditions for species of conservation interest. Depending on sites, and based on the information generated by the stepwise method, designers and managers may decide to exclude life forms of native or non-native species that do not support the growth of a species of conservation interest, or they may create an artificial habitat that is conducive to its persistence.