bluuebunny/crossref_metadata_2025 huggingface dataset:
Substantial Interobserver Agreement in the Diagnosis of Dysplasia in Barrett Esophagus Upon Review of a Patient’s Entire Set of Biopsies
Authors: Salomao Marcela A. , Lam-Himlin Dora , Pai Rish K.
Published: November 2017

The pathologic diagnosis of dysplasia in Barrett esophagus (BE) suffers from interobserver disagreement. Many of the studies demonstrating disagreement in the diagnosis of dysplasia have pathologists review individual biopsy slides in isolation. To more closely mimic daily practice, 3 pathologists reviewed hematoxylin and eosin slides made from 549 individual biopsy jars obtained from 129 unique patients with a diagnosis of BE. Each pathologist reviewed the entirety of a given patient’s biopsy material. The grade of dysplasia present in each biopsy jar was given as well as an overall highest grade of dysplasia from the patient’s entire set of biopsies. The interobserver agreement in the diagnosis of dysplasia per biopsy jar and per patient’s set of biopsies was measured by Fleiss κ statistic for multiple raters. The κ values for each diagnosis was higher in the per patient analysis compared with the per biopsy jar analysis indicating that pathologists are more likely to agree on the overall grade of dysplasia compared with the grade in an individual biopsy jar. In the per patient analysis, the interobserver agreement in the diagnosis of nondysplastic BE and high-grade dysplasia were substantial (κ=0.66; 95% confidence interval [CI], 0.56-0.76 and κ=0.76; 95% CI, 0.66-0.86, respectively). The interobserver agreement in the diagnosis of low-grade dysplasia (LGD) was fair (κ=0.31; 95% CI, 0.21-0.42). When LGD and high-grade dysplasia were collapsed into 1 category of positive for dysplasia, the interobserver agreement in the per patient analysis remained substantial (κ=0.70; 95% CI, 0.60-0.80), suggesting that much of the disagreement in LGD is not due to lack of recognition of dysplastic Barrett’s mucosa, but rather the degree of dysplasia. These results indicate that pathologists can reliably distinguish between nondysplastic BE and dysplastic BE when a patient’s entire set of biopsies is reviewed as a group. When second opinions are obtained, all available slides from that endoscopic procedure should be sent for review.
State-of-the-Art Techniques in Treating Peripheral Nerve Injury
Authors: Kubiak Carrie A. , Kung Theodore A. , Brown David L. , Cederna Paul S. , Kemp Stephen W. P.
Published: November 2017

Background:

Peripheral nerve injuries remain a major clinical concern, as they often lead to chronic disability and significant health care expenditures. Despite advancements in microsurgical techniques to enhance nerve repair, biological approaches are needed to augment nerve regeneration and improve functional outcomes after injury.

Methods:

Presented herein is a review of the current literature on state-of-the-art techniques to enhance functional recovery for patients with nerve injury. Four categories are considered: (1) electroceuticals, (2) nerve guidance conduits, (3) fat grafting, and (4) optogenetics. Significant study results are highlighted, focusing on histologic and functional outcome measures.

Results:

This review documents the current state of the literature. Advancements in neuronal stimulation, tissue engineering, and cell-based therapies demonstrate promise with regard to augmenting nerve regeneration and appropriate rehabilitation.

Conclusions:

The future of treating peripheral nerve injury will include multimodality use of electroconductive conduits, fat grafting, neuronal stimulation, and optogenetics. Further clinical investigation is needed to confirm the efficacy of these technologies on peripheral nerve recovery in humans, and how best to implement this treatment for a diverse population of nerve-injured patients.
Zika virus as a sexually transmitted pathogen
Authors: Mead Paul S. , Hills Susan L. , Brooks John T.
Published: November 2017

Purpose of review

Zika virus has recently emerged from an obscure mosquito-borne pathogen to an international public health concern. It is the first viral agent newly demonstrated to cause birth defects in several decades, and it is the only arbovirus now known to be transmitted sexually. The purpose of this review is to provide an overview of current understanding of sexual transmission of Zika virus and its possible clinical and public health consequences.

Recent findings

Sexual transmission of Zika virus has been reported from at least 13 countries without simultaneous mosquito-borne transmission; it is undoubtedly also occurring in countries with active arthropod transmission. Most published cases involve transmission from symptomatically infected men to women partners. Nevertheless, transmission from a symptomatic man to another man, from a symptomatic woman to a man, and from an asymptomatic man to a woman has also been reported. Sexual transmission has occurred before symptom onset, during illness, and after resolution of the source partner's symptoms. With the exception of a woman who developed symptomatic infection 44 days after onset of her husband's illness, nearly all instances reported to date have occurred within 20 days of the source partner's illness. Zika virus RNA has been detected in semen, saliva, blood, urine, and vaginal and cervical secretions; the length of time during which RNA can be detected varies widely across different body fluids but is especially lengthy in semen. Although semen has been found to contain ZIKV RNA for more than 180 days after illness onset, only a small proportion of samples with detectable RNA yield replicative virus whenever cultured.

Public health agencies have promulgated interim recommendations to prevent sexual transmission of Zika virus; however, much remains unknown regarding the duration of contagiousness and risk factors for transmission. Given the risk for birth defects, the greatest concern is for transmission of the virus to women who are pregnant or attempting to become pregnant. To prevent sexual transmission in general, couples are advised to use condoms or not have sex for at least 6 months from the start of the male partner's symptoms or the date he was diagnosed with Zika or after he has returned from an area with risk of ZIKV infection. Women who have symptomatic ZIKV infection or have traveled to an area of risk are advised to use condoms or avoid sex for 8 weeks from the start of the woman's symptoms or the date she was diagnosed with Zika or after the woman returns from the area of risk.
Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function
Authors: Stubenrauch Christopher J. , Dougan Gordon , Lithgow Trevor , Heinz Eva
Published: November 2017

Fimbriae are long, adhesive structures widespread throughout members of the family Enterobacteriaceae. They are multimeric extrusions, which are moved out of the bacterial cell through an integral outer membrane protein called usher. The complex folding mechanics of the usher protein were recently revealed to be catalysed by the membrane-embedded translocation and assembly module (TAM). Here, we examine the diversity of usher proteins across a wide range of extraintestinal (ExPEC) and enteropathogenic (EPEC)
Escherichia coli
, and further focus on a so far undescribed chaperone–usher system, with this usher referred to as UshC. The fimbrial system containing UshC is distributed across a discrete set of EPEC types, including model strains like E2348/67, as well as ExPEC ST131, currently the most prominent multi-drug-resistant uropathogenic
E. coli
strain worldwide. Deletion of the TAM from a naive strain of
E. coli
results in a drastic time delay in folding of UshC, which can be observed for a protein from EPEC as well as for two introduced proteins from related organisms,
Yersinia
and
Enterobacter
. We suggest that this models why the TAM machinery is essential for efficient folding of proteins acquired via lateral gene transfer.
The
NDE1
genomic locus can affect treatment of psychiatric illness through gene expression changes related to microRNA-484
Authors: Bradshaw Nicholas J. , Ukkola-Vuoti Liisa , Pankakoski Maiju , Zheutlin Amanda B. , Ortega-Alonso Alfredo , Torniainen-Holm Minna , Sinha Vishal , Therman Sebastian , Paunio Tiina , Suvisaari Jaana , Lönnqvist Jouko , Cannon Tyrone D. , Haukka Jari , Hennah William
Published: November 2017

Genetic studies of familial schizophrenia in Finland have observed significant associations with a group of biologically related genes,
DISC1
,
NDE1
,
NDEL1
,
PDE4B
and
PDE4D
, the ‘DISC1 network’. Here, we use gene expression and psychoactive medication use data to study their biological consequences and potential treatment implications. Gene expression levels were determined in 64 individuals from 18 families, while prescription medication information has been collected over a 10-year period for 931 affected individuals. We demonstrate that the
NDE1
SNP rs2242549 associates with significant changes in gene expression for 2908 probes (2542 genes), of which 794 probes (719 genes) were replicable. A significant number of the genes altered were predicted targets of microRNA-484 (
p
= 3.0 × 10
−8
), located on a non-coding exon of
NDE1
. Variants within the
NDE1
locus also displayed significant genotype by gender interaction to early cessation of psychoactive medications metabolized by CYP2C19. Furthermore, we demonstrate that miR-484 can affect the expression of CYP2C19 in a cell culture system. Thus, variation at the
NDE1
locus may alter risk of mental illness, in part through modification of miR-484, and such modification alters treatment response to specific psychoactive medications, leading to the potential for use of this locus in targeting treatment.
Model-based risk assessment and public health analysis to prevent Lyme disease
Authors: Sharareh Nasser , Sabounchi Nasim S. , Roome Amanda , Spathis Rita , Garruto Ralph M.
Published: November 2017

The number of Lyme disease (LD) cases in the northeastern United States has been dramatically increasing with over 300 000 new cases each year. This is due to numerous factors interacting over time including low public awareness of LD, risk behaviours and clothing choices, ecological and climatic factors, an increase in rodents within ecologically fragmented peri-urban built environments and an increase in tick density and infectivity in such environments. We have used a system dynamics (SD) approach to develop a simulation tool to evaluate the significance of risk factors in replicating historical trends of LD cases, and to investigate the influence of different interventions, such as increasing awareness, controlling clothing risk and reducing mouse populations, in reducing LD risk. The model accurately replicates historical trends of LD cases. Among several interventions tested using the simulation model, increasing public awareness most significantly reduces the number of LD cases. This model provides recommendations for LD prevention, including further educational programmes to raise awareness and control behavioural risk. This model has the potential to be used by the public health community to assess the risk of exposure to LD.
Method to improve the survival of night-swarming mayflies near bridges in areas of distracting light pollution
Authors: Egri Ádám , Száz Dénes , Farkas Alexandra , Pereszlényi Ádám , Horváth Gábor , Kriska György
Published: November 2017

Numerous negative ecological effects of urban lighting have been identified during the last decades. In spite of the development of lighting technologies, the detrimental effect of this form of light pollution has not declined. Several insect species are affected including the night-swarming mayflyEphoron virgo: when encountering bridges during their mass swarming, these mayflies often fall victim to artificial lighting. We show a simple method for the conservation of these mayflies exploiting their positive phototaxis. With downstream-facing light-emitting diode beacon lights above two tributaries of the river Danube, we managed to guide egg-laying females to the water and prevent them from perishing outside the river near urban lights. By means of measuring the mayfly outflow from the river as a function of time and the on/off state of the beacons, we showed that the number of mayflies exiting the river's area was practically zero when our beacons were operating. Tributaries could be the sources of mayfly recolonization in case of water quality degradation of large rivers. The protection of mayfly populations in small rivers and safeguarding their aggregation and oviposition sites is therefore important.
Can birds do it too? Evidence for convergence in evaporative water loss regulation for birds and mammals
Authors: Eto E. C. , Withers P. C. , Cooper C. E.
Published: November 2017

Birds have many physiological characteristics that are convergent with mammals. In the light of recent evidence that mammals can maintain a constant insensible evaporative water loss (EWL) over a range of perturbing environmental conditions, we hypothesized that birds might also regulate insensible EWL, reflecting this convergence. We found that budgerigars (Melopsittacus undulatus) maintain EWL constant over a range of relative humidities at three ambient temperatures. EWL, expressed as a function of water vapour pressure deficit, differed from a physical model where the water vapour pressure deficit between the animal and the ambient air is the driver of evaporation, indicating physiological control of EWL. Regulating EWL avoids thermoregulatory impacts of varied evaporative heat loss; changes in relative humidity had no effect on body temperature, metabolic rate or thermal conductance. Our findings that a small bird can regulate EWL are evidence that this is a common feature of convergently endothermic birds and mammals, and may therefore be a fundamental characteristic of endothermy.
Chromatic and achromatic monocular deprivation produce separable changes of eye dominance in adults
Authors: Zhou Jiawei , Reynaud Alexandre , Kim Yeon Jin , Mullen Kathy T. , Hess Robert F.
Published: November 2017

Temporarily depriving one eye of its input, in whole or in part, results in a transient shift in eye dominance in human adults, with the patched eye becoming stronger and the unpatched eye weaker. However, little is known about the role of colour contrast in these behavioural changes. Here, we first show that the changes in eye dominance and contrast sensitivity induced by monocular eye patching affect colour and achromatic contrast sensitivity equally. We next use dichoptic movies, customized and filtered to stimulate the two eyes differentially. We show that a strong imbalance in achromatic contrast between the eyes, with no colour content, also produces similar, unselective shifts in eye dominance for both colour and achromatic contrast sensitivity. Interestingly, if this achromatic imbalance is paired with similar colour contrast in both eyes, the shift in eye dominance is selective, affecting achromatic but not chromatic contrast sensitivity and revealing a dissociation in eye dominance for colour and achromatic image content. On the other hand, a strong imbalance in chromatic contrast between the eyes, with no achromatic content, produces small, unselective changes in eye dominance, but if paired with similar achromatic contrast in both eyes, no changes occur. We conclude that perceptual changes in eye dominance are strongly driven by interocular imbalances in achromatic contrast, with colour contrast having a significant counter balancing effect. In the short term, eyes can have different dominances for achromatic and chromatic contrast, suggesting separate pathways at the site of these neuroplastic changes.
Climate and foraging mode explain interspecific variation in snake metabolic rates
Authors: Dupoué Andréaz , Brischoux François , Lourdais Olivier
Published: November 2017

The energy cost of self-maintenance is a critical facet of life-history strategies. Clarifying the determinant of interspecific variation in metabolic rate (MR) at rest is important to understand and predict ecological patterns such as species distributions or responses to climatic changes. We examined variation of MR in snakes, a group characterized by a remarkable diversity of activity rates and a wide distribution. We collated previously published MR data (n= 491 observations) measured in 90 snake species at different trial temperatures. We tested for the effects of metabolic state (standard MR (SMR) versus resting MR (RMR)), foraging mode (active versus ambush foragers) and climate (temperature and precipitation) while accounting for non-independence owing to phylogeny, body mass and thermal dependence. We found that RMR was 40% higher than SMR, and that active foragers have higher MR than species that ambush their prey. We found that MR was higher in cold environments, supporting the metabolic cold adaptation hypothesis. We also found an additive and positive effect of precipitation on MR suggesting that lower MR in arid environments may decrease dehydration and energetic costs. Altogether, our findings underline the complex influences of climate and foraging mode on MR and emphasize the relevance of these facets to understand the physiological impact of climate change.
Scaling accurate genetic variant discovery to tens of thousands of samples
Authors: Poplin Ryan , Ruano-Rubio Valentin , DePristo Mark A. , Fennell Tim J. , Carneiro Mauricio O. , Van der Auwera Geraldine A. , Kling David E. , Gauthier Laura D. , Levy-Moonshine Ami , Roazen David , Shakir Khalid , Thibault Joel , Chandran Sheila , Whelan Chris , Lek Monkol , Gabriel Stacey , Daly Mark J , Neale Ben , MacArthur Daniel G. , Banks Eric
Published: November 2017

Comprehensive disease gene discovery in both common and rare diseases will require the efficient and accurate detection of all classes of genetic variation across tens to hundreds of thousands of human samples. We describe here a novel assembly-based approach to variant calling, the GATK HaplotypeCaller (HC) and Reference Confidence Model (RCM), that determines genotype likelihoods independently per-sample but performs joint calling across all samples within a project simultaneously. We show by calling over 90,000 samples from the Exome Aggregation Consortium (ExAC) that, in contrast to other algorithms, the HC-RCM scales efficiently to very large sample sizes without loss in accuracy; and that the accuracy of indel variant calling is superior in comparison to other algorithms. More importantly, the HC-RCM produces a fully squared-off matrix of genotypes across all samples at every genomic position being investigated. The HC-RCM is a novel, scalable, assembly-based algorithm with abundant applications for population genetics and clinical studies.
Combined flow cytometry and high throughput image analysis for the study of essential genes in Caenorhabditis elegans
Authors: Hernando-Rodríguez Blanca , Erinjeri Annmary Paul , Rodríguez-Palero María Jesús , Millar Val , González-Hernández Sara , Olmedo María , Schulze Bettina , Baumeister Ralf , Muñoz Manuel J. , Askjaer Peter , Artal-Sanz Marta
Published: November 2017

Background

The advancement in automated image based microscopy platforms coupled with high throughput liquid workflows has facilitated the design of large scale screens utilizing multicellular model organisms such as Caenorhabditis elegans to identify genetic interactions, therapeutic drugs or disease modifiers. However, the analysis of essential genes has lagged behind because lethal or sterile mutations pose a bottleneck for high throughput approaches.

Results

In C. elegans, non-conditional lethal mutations can be maintained in heterozygosis using chromosome balancers, commonly labelled with GFP in the pharynx. Moreover gene-expression is typically monitored by the use of fluorescent reporters marked with the same fluorophore. Therefore, the separation of the different populations of animals at early larval stages represents a challenge. Here, we develop a sorting strategy capable of selecting homozygous mutants carrying a GFP stress reporter from GFP-balanced animals at early larval stages. Because sorting is not completely error-free, we develop an automated high-throughput image-analysis protocol that identifies and discards animals carrying the chromosome balancer. We demonstrate the experimental usefulness of combining sorting of homozygous lethal mutants and automated image-analysis in a functional genomic RNAi screen for genes that genetically interact with mitochondrial prohibitin (PHB). Lack of PHB results in embryonic lethality, while, homozygous PHB deletion mutants develop into sterile adults due to maternal contribution and strongly induce the mitochondrial unfolded protein response (UPRmt). In a chromosome-wide RNAi screen for C. elegans genes having human orthologues, we uncover both, known and new PHB genetic interactors affecting the UPRmt and growth.

Conclusions

A systematic way to analyse genetic interactions of essential genes in multicellular organisms is lacking. The method presented here allows the study of balanced lethal mutations in a high-throughput manner and can be easily adapted depending on the user’s requirements. Therefore, it will serve as a useful resource for the C. elegans community for probing new biological aspects of essential nematode genes as well as the generation of more comprehensive genetic networks.
A systems approach to refine disease taxonomy by integrating phenotypic and molecular networks
Authors: Zhou Xuezhong , Lei Lei , Liu Jun , Halu Arda , Zhang Yingying , Li Bing , Guo Zhili , Liu Guangming , Sun Changkai , Loscalzo Joseph , Sharma Amitabh , Wang Zhong
Published: November 2017

The International Classification of Diseases (ICD) relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD) by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles. With statistical validations from phenotype-genotype associations and interactome networks, we demonstrate that NCD improves disease specificity owing to its overlapping categories and polyhierarchical structure. Furthermore, NCD captures the molecular diversity of diseases and defines clearer boundaries in terms of both phenotypic similarity and molecular associations, establishing a rational strategy to reform disease taxonomy.
Structure and function of accessory Sec proteins involved in the adhesin export pathway of Streptococcus gordonii
Authors: Chen Yu , Bensing Barbara A. , Seepersaud Ravin , Mi Wei , Liao Maofu , Jeffrey Philip D. , Shajahan Asif , Sonon Roberto N. , Azadi Parastoo , Sullam Paul M. , Rapoport Tom A.
Published: November 2017

Many pathogenic bacteria, includingStreptococcus gordonii, possess a pathway for the export of a single serine-rich-repeat protein that mediates the adhesion of bacteria to host cells and the extracellular matrix. These adhesins areO-glycosylated by several cytosolic glycosyltransferases and require three accessory Sec proteins (Asp1-3) for export, but how the adhesins are processed for secretion is not well defined. Here, we show thatO-glycosylation ofS. gordoniiadhesin GspB occurs in a sequential manner by three enzymes (GtfA/B, Nss, Gly) that attach N-acetylglucosamine and glucose to Ser/Thr residues. The modified substrate is subsequently transferred from the last glycosyltransferase to the Asp1/2/3 complex. Crystal structures show that both Asp1 and Asp3 are related to carbohydrate binding proteins. Asp1 also has an affinity for phospholipids, which is attenuated by Asp2. These results suggest a mechanism for the modification of adhesin in the cytosol and its subsequent targeting to the export machinery.
Discrete and continuum approximations for collective cell migration in a scratch assay with cell size dynamics
Authors: Matsiaka Oleksii M , Penington Catherine J , Baker Ruth E , Simpson Matthew J
Published: November 2017

Scratch assays are routinely used to study the collective spreading of cell populations. In general, the rate at which a population of cells spreads is driven by the combined effects of cell migration and proliferation. To examine the effects of cell migration separately from the effects of cell proliferation, scratch assays are often performed after treating the cells with a drug that inhibits proliferation. Mitomycin-C is a drug that is commonly used to suppress cell proliferation in this context. However, in addition to suppressing cell proliferation, Mitomycin-C also causes cells to change size during the experiment, as each cell in the population approximately doubles in size as a result of treatment. Therefore, to describe a scratch assay that incorporates the effects of cell-to-cell crowding, cell-to-cell adhesion, and dynamic changes in cell size, we present a new stochastic model that incorporates these mechanisms. Our agent-based stochastic model takes the form of a system of Langevin equations that is the system of stochastic differential equations governing the evolution of the population of agents. We incorporate a time-dependent interaction force that is used to mimic the dynamic increase in size of the agents. To provide a mathematical description of the average behaviour of the stochastic model we present continuum limit descriptions using both a standard mean-field approximation, and a more sophisticated moment dynamics approximation that accounts for the density of agents and density of pairs of agents in the stochastic model. Comparing the accuracy of the two continuum descriptions for a typical scratch assay geometry shows that the incorporation of agent growth in the system is associated with a decrease in accuracy of the standard mean-field description. In contrast, the moment dynamics description provides a more accurate prediction of the evolution of the scratch assay when the increase in size of individual agents is included in the model.
The nature of nurture: effects of parental genotypes
Authors: Kong Augustine , Thorleifsson Gudmar , Frigge Michael L. , Vilhjálmsson Bjarni J. , Young Alexander I. , Thorgeirsson Thorgeir E. , Benonisdottir Stefania , Oddsson Asmundur , Halldórsson Bjarni V. , Masson Gísli , Gudbjartsson Daniel F. , Helgason Agnar , Bjornsdottir Gyda , Thorsteinsdottir Unnur , Stefansson Kari
Published: November 2017

Sequence variants in the parental genomes that are not transmitted to a child/proband are often ignored in genetic studies. Here we show that non-transmitted alleles can impact a child through their effects on the parents and other relatives, a phenomenon we call genetic nurture. Using results from a meta-analysis of educational attainment, the polygenic score computed for the non-transmitted alleles of 21,637 probands with at least one parent genotyped has an estimated effect on the educational attainment of the proband that is 29.9% (P= 1.6×10−14) of that of the transmitted polygenic score. Genetic nurturing effects of this polygenic score extend to other traits. Paternal and maternal polygenic scores have similar effects on educational attainment, but mothers contribute more than fathers to nutrition/heath related traits.

One Sentence Summary

Nurture has a genetic component,i.e.alleles in the parents affect the parents’ phenotypes and through that influence the outcomes of the child.
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
Authors: Keilwagen Jens , Hartung Frank , Paulini Michael , Twardziok Sven O. , Grau Jan
Published: November 2017

Motivation

Genome annotation is of key importance in many research questions. The identification of protein-coding genes is often based on transcriptome sequencing data, ab-initio or homology-based prediction. Recently, it was demonstrated that intron position conservation improves homology-based gene prediction, and that experimental data improves ab-initio gene prediction.

Results

Here, we present an extension of the gene prediction tool GeMoMa that utilizes amino acid sequence conservation, intron position conservation and optionally RNA-seq data for homology-based gene prediction. We show on published benchmark data for plants, animals and fungi that GeMoMa performs better than the gene prediction programs BRAKER1, MAKER2, and CodingQuarry, and purely RNA-seq-based pipelines for transcript identification. In addition, we demonstrate that using multiple reference organisms may help to further improve the performance of GeMoMa. Finally, we apply GeMoMa to four nematode species and to the recently published barley reference genome indicating that current annotations of protein-coding genes may be refined using GeMoMa predictions.

Availability

GeMoMa has been published under GNU GPL3 and is freely available at http://www.jstacs.de/index.php/GeMoMa.

Contact

jens.keilwagen@julius-kuehn.de
Potent and Selective Antitumor Activity of a T-Cell Engaging Bispecific Antibody Targeting a Membrane-Proximal Epitope of ROR1
Authors: Qi Junpeng , Li Xiuling , Peng Haiyong , Park HaJeung , Rader Christoph
Published: November 2017

T-cell engaging bispecific antibodies present a promising strategy for cancer immunotherapy and numerous bispecific formats have been developed for retargeting cytolytic T cells toward tumor cells. To explore the therapeutic utility of T-cell engaging bispecific antibodies targeting the receptor tyrosine kinase ROR1, which is expressed by tumor cells of various hematologic and solid malignancies, we used a bispecific ROR1 × CD3 scFv-Fc format based on a heterodimeric and aglycosylated Fc domain designed for extended circulatory half-life and diminished systemic T-cell activation. A diverse panel of ROR1-targeting scFv derived from immune and naïve rabbit antibody repertoires was compared in this bispecific format for target-dependent T-cell recruitment and activation. A ROR1-targeting scFv with a membrane-proximal epitope, R11, revealed potent and selective antitumor activityin vitroandin vivoand emerged as a prime candidate for further preclinical and clinical studies. To elucidate the precise location and engagement of this membrane-proximal epitope, which is conserved between human and mouse ROR1, the three-dimensional structure of scFv R11 in complex with the kringle domain of ROR1 was determined by X-ray crystallography at 1.6-Å resolution.
Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge
Authors: Saul Michael C. , Blatti Charles , Yang Wei , Bukhari Syed Abbas , Shpigler Hagai Y. , Troy Joseph M. , Seward Christopher H. , Sloofman Laura , Chandrasekaran Sriram , Bell Alison M. , Stubbs Lisa , Robinson Gene E. , Zhao Sihai Dave , Sinha Saurabh
Published: November 2017

Social challenges like territorial intrusions evoke behavioral responses in widely diverging species. Recent work has revealed that evolutionary “toolkits” – genes and modules with lineage-specific variations but deep conservation of function – participate in the behavioral response to social challenge. Here, we develop a multi-species computational-experimental approach to characterize such a toolkit at a systems level. Brain transcriptomic responses to social challenge was probed via RNA-seq profiling in three diverged species – honey bees, mice, and three-spined stickleback fish – following a common methodology, allowing fair comparisons across species. Data were collected from multiple brain regions and multiple time points after social challenge exposure, achieving anatomical and temporal resolution substantially greater than previous work. We developed statistically rigorous analyses equipped to find homologous functional groups among these species at the levels of individual genes, functional and coexpressed gene modules, and transcription factor sub-networks. We identified six orthogroups involved in response to social challenge, including groups represented by mouse genes Npas4 and Nr4a1, as well as common modulation of systems such as transcriptional regulators, ion channels, G-protein coupled receptors, and synaptic proteins. We also identified conserved coexpression modules enriched for mitochondrial fatty acid metabolism and heat shock that constitute the shared neurogenomic response. Our analysis suggests a toolkit wherein nuclear receptors, interacting with chaperones, induce transcriptional changes in mitochondrial activity, neural cytoarchitecture, and synaptic transmission after social challenge. It reveals systems-level mechanisms that have been repeatedly co-opted during evolution of analogous behaviors, thus advancing the genetic toolkit concept beyond individual genes.
Genetic Single Neuron Anatomy reveals fine granularity of cortical interneuron subtypes
Authors: Wang Xiaojun , Tucciarone Jason , Jiang Siqi , Yin Fangfang , Wang Bor-shuen , Wang Dingkang , Jia Yao , Jia Xueyan , Li Yuxin , Yang Tao , Xu Zhengchao , Akram Masood A. , Wang Yusu , Zeng Shaoqun , Ascoli Giorgio A. , Mitra Partha , Gong Hui , Luo Qingming , Huang Z. Josh
Published: November 2017

Parsing diverse nerve cells into biological types is necessary for understanding neural circuit organization. Morphology is an intuitive criterion for neuronal classification and a proxy of connectivity, but morphological diversity and variability often preclude resolving the granularity of discrete cell groups from population continuum. Combining genetic labeling with high-resolution, large volume light microscopy, we established a platform of genetic single neuron anatomy that resolves, registers and quantifies complete neuron morphologies in the mouse brain. We discovered that cortical axo-axonic cells (AACs), a cardinal GABAergic interneuron type that controls pyramidal neuron (PyN) spiking at axon initial segment, consist of multiple subtypes distinguished by laminar position, dendritic and axonal arborization patterns. Whereas the laminar arrangements of AAC dendrites reflect differential recruitment by input streams, the laminar distribution and local geometry of AAC axons enable differential innervation of PyN ensembles. Therefore, interneuron types likely consist of fine-grained subtypes with distinct input-output connectivity patterns.
The dynamics of starvation and recovery
Authors: Yeakel Justin D. , Kempes Christopher P. , Redner Sidney
Published: November 2017

The eco-evolutionary dynamics of species are fundamentally linked to the energetic constraints of its constituent individuals. Of particular importance is the interplay between reproduction and the dynamics of starvation and recovery. To elucidate this interplay, we introduce a nutritional state-structured model that incorporates two classes of consumer: nutritionally replete, reproducing consumers, and undernourished, non-reproducing consumers. We obtain strong constraints on starvation and recovery rates by deriving allometric scaling relationships and find that population dynamics are typically driven to a steady state. Moreover, these rates fall within a ‘refuge’ in parameter space, where the probability of population extinction is minimized. We also show that our model provides a natural framework to predict maximum mammalian body size by determining the relative stability of an otherwise homogeneous population to a competing population with altered percent body fat. This framework provides a principled mechanism for a selective driver of Cope’s rule.
High-throughput sequencing of murine immunoglobulin heavy chain transcripts using single side unique molecular identifiers on an Ion Torrent PGM
Authors: Bürckert Jean-Philippe , Faison William J. , Dubois Axel R. S. X. , Sinner Regina , Hunewald Oliver , Wienecke-Baldacchino Anke , Brieger Anne , Muller Claude P.
Published: November 2017

With the advent of high-throughput sequencing (HTS), profiling immunoglobulin (IG) repertoires has become an essential part of immunological research. Advances in sequencing technology enable the IonTorrent Personal Genome Machine (PGM) to cover the full-length of IG mRNA transcripts. Nucleotide insertions and deletions (indels) are the dominant errors of the PGM sequencing platform and can critically influence IG repertoire assessments. Here, we present a PGM-tailored IG repertoire sequencing approach combining error correction through unique molecular identifier (UID) barcoding and indel detection through ImMunoGeneTics (IMGT), the most commonly used sequence alignment database for IG sequences. Using artificially falsified sequences for benchmarking, we found that IMGT efficiently detects 98% of the introduced indels through gene-segment frameshifts. Undetected indels are either located at the ends of the sequences or produce masked frameshifts with an insertion and deletion in close proximity. IMGT’s indel correction algorithm resolves up to 87% of the tested insertions, but no deletions. The complementary determining regions 3 (CDR3s) are returned 100% correct for up to 3 insertions or 3 deletions through conservative culling. We further show, that our PGM-tailored unique molecular identifiers results in highly accurate HTS datasets if combined with the presented data processing. In this regard, considering sequences with at least two copies from datasets with UID families of minimum 3 reads result in correct sequences with over 99% confidence. The protocol and sample processing strategies described in this study will help to establish benchtop-scale sequencing of IG heavy chain transcripts in the field of IG repertoire research.
Quantifying Immune-Based Counterselection of Somatic Mutations
Authors: Yang Fan , Kim Dae-Kyum , Nakagawa Hidewaki , Hayashi Shuto , Imoto Seiya , Stein Lincoln , Roth Frederick P.
Published: November 2017

It is now well established that somatic mutations in protein-coding regions can generate ‘neoantigens’, and that these can be recognized by the immune system and contribute to clearance of developing cancers. However, there is currently no model that can quantitatively predict the neoantigenic effect of any given somatic mutation. Here, we examined signatures of immune selection pressure on the distribution of somatic mutations. We quantified the extent to which somatic mutations are significantly depleted in peptides that are predicted to be displayed by major histocompatibility complex (MHC) class I proteins. We characterized the dependence of this depletion on expression level. We then examined whether immune selection pressure on somatic mutations changes depending on whether the patient had either one or two MHC-encoding alleles that can display the peptide. Our results indicate that MHC-encoding alleles are, in general, incompletely dominant, i.e., that having two copies of the display-enabling allele is more effective in displaying that peptide than having just one copy. More generally, a quantitative understanding of counter-selection of identifiable subclasses of neoantigenic somatic variation could guide immunotherapy or aid in developing personalized cancer vaccines.
COLT-Viz: Interactive Visualization of Antibody Lineage Trees
Authors: He Chenfeng , Wendel Ben S. , Xiao Jun , Chen Keke , Jiang Ning
Published: November 2017

Many tools have been developed to visualize phylogenetic trees, which is a traditional technique for evolutionary tree analysis. However, due to the unique characteristics of antibody lineage trees, the phylogenetic method cannot adequately construct proper tree structures for antibody lineages, and many other tools have been developed to address this problem. However, there still lacks of an adequate tool to visualize the resulted antibody lineage structures that are more complicated than phylogenetic trees. In addition, high-throughput sequencing-based antibody repertoire profiling enables the counting of the number of transcripts associated with individual antibody sequences, thus more dimensions need to be encoded in the tree structure visualization. Further, users may wish to manually adjust the tree structure for a special context. When doing so, they may wish to maintain some biological constraints that are applicable in antibody lineage tree structure, such as isotype switching constraints or different sampling constraints. Here, we report an interactive visualization tool (COLT-Viz) designed to display the number of RNA copies, number of somatic hypermutations, and sample collection time associated with each antibody sequence as well as the distance to neighboring sequences for each antibody sequence in the lineage. COLT-Viz also allows users to interactively visualize and edit antibody lineage structures while giving users the option to automatically check biological constraints on the edited structures to ensure accuracy. COLT-Viz takes JSON text format as input files and can easily be used to visualize networks with or without the biological constraints. We believe the amount of information that can be displayed for complex antibody lineages, the interactive interface, and the option of checking for biological constraints make COLT-Viz a versatile tool for antibody lineage tree visualization that will guide further biological discoveries.
Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in
Authors: Chen Yi-Jiun , Wang Weikang , Tian Xiao-Jiun , Lefever Daniel E. , Taft David A. , Xing Jianhua
Published: November 2017

CRISPR-based gene knock-in at endogenous sites is desirable in multiple fields such as quantitative studies of signal transduction pathways and gene regulation, synthetic biology, and disease modeling. Contrasting the knock-out procedure, a key step of CRISPR knock-in procedure relies on the homology-directed repairing (HDR) process that requires a donor construct as repair template. Therefore, it is desirable to generate a series of donor DNA constructs efficiently and cost-effectively. In this study, we developed a general Gibson assembly procedure that combines strengths of a Modular Overlap-Directed Assembly with Linkers (MODAL) strategy and a restriction enzyme based hierarchical framework. This procedure also allows fusing sgRNAs to the constructs for enhanced homology-directed repairing efficiency. Experimental tests on multiple constructs achieved from 3-8 folds of increase in assembly efficiency to high yield of constructs that failed to make with conventional Gibson assembly. The modularized procedure is simple, fast and cost-effective while making multiple constructs, and a computer package is provided for customized design.
Hoxgenes pattern the primary body axis of an anthozoan cnidarian prior to gastrulation
Authors: DuBuc Timothy Q. , Stephenson Thomas B. , Rock Amber Q. , Martindale Mark Q.
Published: November 2017

Hoxgene transcription factors are important regulators of positional identity along the anterior-posterior axis in bilaterian animals. Cnidarians (e.g. sea anemones, corals and hydroids) are the sister group to the Bilateria and possess genes related to both anterior and central/posterior classHoxgenes. In the absence of a conserved set ofHoxgenes among other early branching animal clades, cnidarians provide the best opportunity to learn about the emergence of this gene family. We report a previously unrecognized domain ofHoxexpression in the starlet sea anemone,Nematostella vectensis, beginning at early blastula stages. Functional perturbation reveals that twoHoxgenes not only regulate their respective expression domains, but interact with one another to pattern the entire oral-aboral axis mediated by Wnt signaling. This suggests an ancient link betweenHox/Wntpatterning of the oral-aboral axis and suggest that these domains are likely established during blastula formation in anthozoan cnidarians.
Orientational disorder and phase transitions in ammonium oxofluorovanadates, (NH4)3VOF5 and (NH4)3VO2F4
Authors: Udovenko Anatoly A. , Pogoreltsev Evgeny I. , Marchenko Yuri V. , Laptash Natalia M.
Published: November 2017

Single crystals of (NH4)3VOF5 and (NH4)3VO2F4 were obtained from aqueous fluoride solutions and phase transitions in these compounds were investigated using X-ray diffraction, differential scanning microcalorimetry (DSM) and vibrational spectroscopy. The room-temperature (RT) phases of these compounds belong to orthorhombic symmetry [Immm and I222, Z = 6, for (NH4)3VOF5 and (NH4)3VO2F4, respectively] with similar unit-cell parameters and two independent vanadium atoms. Above RT [at 350 and 440 K for (NH4)3VOF5 and (NH4)3VO2F4, respectively], the compounds undergo reversible phase transitions into high-symmetry dynamically disordered elpasolite-like (Fm{\bar 3}m, Z = 4) structures with six and 12 spatial orientations of the vanadium octahedron for (NH4)3VOF5 and (NH4)3VO2F4, respectively. The ligand atoms are distributed in a mixed (split) position of 24e + 96j, one of the ammonium groups is disordered on the tetrahedron 32f site, but another one forms eight spatial orientations due to disorder of its hydrogen atoms in the 96j position. DSM and spectroscopic data enable the phase transition from high temperature to room temperature to be connected with the transition from isotropic orientations of the octahedron to its two different dynamic states.
Engaging workforce in downsized firms: scenario of the Indian IT/ITES sector
Authors: Tiwari Binita , Lenka Usha
Published: November 2017

Purpose

Organisations increasingly reduce enterprise costs via cost cutting measures of downsizing/layoffs as a short-term strategy. The purpose of this paper is to illustrate the scenario of downsizing in the Indian IT/ITES sector and also identify enablers to develop and engage talent in downsized firms.

Design/methodology/approach

This paper is a general review.

Findings

Despite higher growth rates in the recent years, the IT/ITES sector faces an uncertain future due to economic recession, which has changed the business scenario across the globe. Organisations need to resuscitate employees’ confidence and self-efficacy through psychosocial support mechanisms like professional guidance by an emotionally intelligent leader, capacity-building measures, and continuous learning opportunities. They should prepare scheduled reviews by taking into account individual needs, learning styles, and current work priorities. Provisions for adequate pay, fringe benefits, job security, and healthy working conditions can further enhance morale and motivation of survivors.

Originality/value

This paper contributes to the literature of downsizing in the Indian context. Moreover, it emphasises on the significant roles of communication policies, knowledge sharing, and learning in rebuilding the psychological contract of employees.