bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corneal Biomechanical Alterations in Patients with Chronic Ocular Graft Versus-host Disease
Authors: Giannaccare Giuseppe , Pellegrini Marco , Taroni Leonardo , Bernabei Federico , Senni Carlotta , Grendele Arianna , Scorcia Vincenzo , Campos Emilio C 
Published: February 2019

AbstractPurposeTo compare corneal biomechanics between patients with ocular graft versus-host disease (oGVHD) and healthy subjects (controls), and to further correlate these values with ocular and hematological characteristics.Materials and MethodsThe following procedures were performed in oGVHD patients and controls: Schirmer test (ST), break-up time (BUT), corneal and conjunctival staining, tear matrix metalloproteinase-9 (MMP-9) assay (InflammaDry test, Rapid Pathogen Screening, Inc, Sarasota, FL). Corneal biomechanics were calculated by using ocular response analyzer (ORA, Reichert Instruments, Depew, New York, USA). The Mann-Whitney U test was used to compare continuous variables between oGVHD patients and controls. Correlations of corneal biomechanics with ocular and hematological parameters were examined using Spearman’s correlation.ResultsA total of 45 oGVHD patients (mean age ± SD, 51.5 ± 7.1 years) and 34 controls (47.8 ± 6.1 years) were included. Patients with oGVHD showed significantly lower values of corneal hysteresis (CH) and corneal resistance factor (CRF) compared to controls (respectively, 9.4 ± 1.8 mmHg vs 11.6 ± 1.6 and 9.7 ± 1.4 mmHg vs 12.3 ± 1.3; alwaysp<0.001). Twenty-nine of the oGVHD eyes (64.4%) were strong-positive for MMP-9, while 16 (35.6%) were weak-positive. Conversely, only 4 of the control eyes (11.8%) were weak-positive for MMP-9. In patients with oGVHD, CH was significantly correlated with corneal staining (Rs= −0.316,p= 0.035), conjunctival staining (Rs= −0.437,p= 0.003), ST (Rs= 0.390,p= 0.008), BUT (Rs= 0.423,p= 0.004), oGVHD severity grade (Rs = −0.383,p= 0.009), and MMP-9 positivity grade (Rs= −0.429,p= 0.003), while CRF was correlated only with corneal staining (Rs= −0.317,p= 0.034).ConclusionsCorneal biomechanics are reduced in patients with oGVHD, and CH is negatively correlated with disease severity grade and MMP-9 tear levels.
The Process Pathway Model of bacterial growth
Authors: Biro Daniel , Pechuan Ximo , Lambros Maryl , Bergman Aviv 
Published: February 2019

AbstractThe growth profile of microorganisms in an enclosed environment, such as a bioreactor or flask, is a well studied and characterized system. Despite a long history of examination, there are still many competing mathematical models used to describe an output of the microorganisms, namely the number of bacteria as a function of time. However, these descriptions are either purely phenomenological and give no intuition as to the biological mechanisms underlying the growth curves, or extremely complex and become computationally unfeasible at the population level. In this paper, we develop the Process Pathway Model by modifying a model of sequential processes, which was first used to model robustness in metabolic pathways, and demonstrate that the Process Pathway Model encapsulates many features and temperature dependence of bacterial growth. We verify the predictions of the model against growth data for multiple species of microorganisms, and confirm that the model generates accurate predictions on temperature dependence of bacterial growth. The model has five free parameters, and the simplifying assumptions used to build the model are built upon biologically realistic notions. The Process Pathway Model accurately models a microorganism’s growth profile at an intermediate level of complexity that is computationally feasible. This model can be used as both an conceptual model for thinking about systems of bacterial growth, as well as a computational model that operates at level of complexity that is amenable to large scale simulation. This balance in accuracy and intuitiveness was accomplished by using realistic biological assumptions to simplify the underlying biology, which may point the way forward for future models of this type.
Evaluating Invasive EEG Implantations in Medically Refractory Epilepsy with Functional Scalp EEG Recordings and Structural Imaging Data
Authors: Palepu Anil , Li Adam , Fitzgerald Zachary , Hu Katherine , Costacurta Julia , Bulacio Juan , Martinez-Gonzalez Jorge , Sarma Sridevi V. 
Published: February 2019

AbstractSeizures in patients with medically refractory epilepsy (MRE) epilepsy cannot be controlled with drugs. For focal MRE, seizures originate in the epileptogenic zone (EZ), which is the minimum amount of cortex that must be treated to be seizure free. Localizing the EZ is often a laborious process wherein clinicians first inspect scalp EEG recordings during several seizure events, and then formulate an implantation plan for subsequent invasive monitoring. The goal of implantation is to place electrodes into the brain region covering the EZ. Then, during invasive monitoring, clinicians visually inspect intracranial EEG recordings to more precisely localize the EZ. The EZ is then surgically removed. Unfortunately surgical success rates average at 50%. Such grim outcomes call for analytical assistance in creating more accurate implantation plans from scalp EEG. In this paper, we introduce a method that combines imaging data (CT and MRI scans) with scalp EEG to derive an implantation distribution. Specifically, scalp EEG data recorded over a seizure event is converted into a time-gamma frequency map, which is then processed to derive a spectrally annotated implantation distribution (SAID). The SAID represents a distribution of gamma power in each of the eight cortical lobe/hemisphere partitions. We applied this method to 4 MRE patients who underwent treatment, and found that the SAID distribution overlapped more with clinical implantations in success cases than in failed cases. These preliminary findings suggest that the SAID may help in improving EZ localization accuracy and surgical outcomes.
A late Permian ichthyofauna from the Zechstein Basin, Lithuania-Latvia Region
Authors: Dankina-Beyer Darja , Spiridonov Andrej , Stinkulis Ģirts , Manzanares Esther , Radzevičius Sigitas 
Published: February 2019

AbstractThe late Permian is a transformative time, which ended in one of the most significant extinction events in Earth’s history. Fish assemblages are a major component of marine foods webs. The macroevolution and biogeographic patterns of late Permian fish are currently insufficiently known. In this contribution, the late Permian fish fauna from Kūmas quarry (southern Latvia) is described for the first time. As a result, the studied late Permian Latvian assemblage consisted of isolated chondrichthyan teeth ofHelodussp., ?Acrodussp., ?Omanoselachesp. and euselachian type dermal denticles as well as many osteichthyan scales of the Haplolepidae and Elonichthydae; numerous teeth ofPalaeoniscus, rare teeth findings of ?Platysomussp. and many indeterminate microremains. This ichthyofaunal assemblage is very similar to the contemporaneous Lopingian complex of the carbonate formation from the Karpėnai quarry (northern Lithuania), despite the fact that Kūmas samples include higher diversity and abundance in fossil remains. The differences in abundance of microremains could possibly be explained by a fresh water influx in the northeastern Zechstein Basin margin, which probably reduced the salinity of the sea water. The new data enable a better understanding of the poorly known late Permian fish diversity from the Lithuania-Latvia Region.
Viruses rule over adaptation in conserved human proteins
Authors: Castellano David , Uricchio Lawrence H. , Munch Kasper , Enard David 
Published: February 2019

AbstractAdaptive evolution often involves fast-evolving proteins, and the fastest-evolving proteins in primates include antiviral proteins engaged in an arms race with viruses1-3. Even though fast-evolving antiviral proteins are the most studied cases of primate host adaptation against viruses, viruses predominantly interact with host proteins that are broadly conserved between distant species in order to complete their replication cycle4. Broadly conserved proteins are generally viewed as playing a negligible role in adaptive evolution. Here, we used a dataset of ~4,500 human proteins known to physically interact with viruses (VIPs for Virus-Interacting Proteins), to test the involvement of broadly conserved proteins in adaptive evolution against viruses. We found that VIPs conserved between animals and fungi have experienced not only high rates of adaption, but also strong adaptive events. Broadly conserved proteins that do not interact with viruses experienced very little adaptation. As a result, the arms race with viruses explains more than 75% of adaptation in the most phylogenetically conserved subset of the human proteome. Our results imply that broadly conserved proteins have played a significant role in adaptation, and that viruses were likely one of very few selective pressures that were able to force the conserved, central pillars of host cellular functions to adapt during evolution.
Case-only analysis of gene-environment interactions using polygenic risk scores
Authors: Meisner Allison , Kundu Prosenjit , Chatterjee Nilanjan 
Published: February 2019

AbstractInvestigations of gene (G)-environment (E) interactions have led to limited findings to date, possibly due to weak effects of individual genetic variants. Polygenic risk scores (PRS), which capture the genetic susceptibility associated with a set of variants, can be a powerful tool for detecting global patterns of interaction. Motivated by the case-only method for evaluating interactions with a single variant, we propose a case-only method for the analysis of interactions with a PRS in case-control studies. Assuming the PRS and E are independent, we show how a linear regression of the PRS on E in a sample of cases can be used to efficiently estimate the interaction parameter. Furthermore, if an estimate of the mean of the PRS in the underlying population is available, the proposed method can estimate the PRS main effect. Extensions allow for PRS-E dependence due to associations between variants in the PRS and E. Simulation studies indicate the proposed method offers appreciable gains in efficiency over logistic regression and can recover much of the efficiency of a cohort study. As an illustration, we apply the proposed method to investigate interactions between a PRS and epidemiologic factors on breast cancer risk in the UK Biobank study.
Transcriptome stability profiling using 5’-bromouridine IP chase (BRIC-seq) identifies novel and functional microRNA targets in human melanoma cells
Authors: Joshi Piyush , Seki Tatsuya , Kitamura Shinobu , Bergano Andrea , Lee Bongyong , Perera Ranjan J. 
Published: February 2019

ABSTRACTRNA half-life is closely related to its cellular physiological function, so stability determinants may have regulatory functions. Micro(mi)RNAs have primarily been studied with respect to post-transcriptional mRNA regulation and target degradation. Here we study the impact of the tumor suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. Using 5’-bromouridine IP chase (BRIC)-seq, transcriptome-wide RNA stability profiles revealed highly regulated genes and pathways important in this melanoma cell line. By combining BRIC-seq, RNA-seq and in silico predictions, we identified both existing and novel direct miR-211 targets. We validated DUSP3 as one such novel miR-211 target, which itself sustains colony formation and invasion in A375 cells via MAPK/PI3K signaling. miRNAs have the capacity to control RNA turnover as a gene expression mechanism, and RNA stability profiling is an excellent tool for interrogating functionally relevant gene regulatory pathways and miRNA targets when combined with other high-throughput and in silico approaches.
A single-cell reference map for human blood and tissue T cell activation reveals functional states in health and disease
Authors: Szabo Peter A. , Levitin Hanna Mendes , Miron Michelle , Snyder Mark E. , Senda Takashi , Yuan Jinzhou , Cheng Yim Ling , Bush Erin C. , Dogra Pranay , Thapa Puspa , Farber Donna L. , Sims Peter A. 
Published: February 2019

ABSTRACTHuman T cells coordinate adaptive immunity by localization in diverse tissue sites, though blood T cells are the most readily studied. Here, we used single-cell RNA-seq to define the functional responses of T cells isolated from human lungs, lymph nodes, bone marrow, and blood to TCR-stimulation. We reveal how human T cells in tissues relate to those in blood, and define activation states for CD4+ and CD8+T cells across all sites, including an interferon-response state for CD4+T cells and distinct effector states for CD8+T cells. We further show how profiles of individual tumor-associated T cells can be projected onto this healthy reference map, revealing their functional state.
The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor
Authors: LeVine Michael V. , Terry Daniel S. , Khelashvili George , Siegel Zarek S. , Quick Matthias , Javitch Jonathan A. , Blanchard Scott C. , Weinstein Harel 
Published: February 2019

AbstractNeurotransmitter:sodium symporters (NSS) in the SLC6 family terminate neurotransmission by coupling the thermodynamically favorable transport of ions to the thermodynamically unfavorable transport of neurotransmitter back into presynaptic neurons. While a combination of structural, functional, and computational studies on LeuT, a bacterial NSS homolog, has provided critical insight into the mechanism of sodium-coupled transport, the mechanism underlying substrate-specific transport rates is still not understood. We present a combination of MD simulations, single-molecule FRET imaging, and measurements of Na+ binding and substrate transport that reveal an allosteric mechanism in which residues F259 and I359 in the substrate binding pocket couple substrate binding to Na+ release from the Na2 site through allosteric modulation of the stability of a partially-open, inward-facing state. We propose a new model for transport selectivity in which the two residues act as a volumetric sensor that inhibits the transport of bulky amino acids.
IL-27 receptor signaling regulated stress myelopoiesis drives Abdominal Aortic Aneurysm development
Authors: Peshkova Iuliia O. , Aghayev Turan , Fatkhullina Aliia R. , Makhov Petr , Eguchi Satoru , Tan Yin Fei , Kossenkov Andrew V. , Sykes Stephen , Koltsova Ekaterina K. 
Published: February 2019

AbstractAbdominal Aortic Aneurysm (AAA) is a vascular disease, where aortic wall degradation is mediated by accumulated immune cells. Though cytokines regulate the inflammatory milieu within the aortic wall, their contribution to AAA through distant alterations, particularly in the control of hematopoietic stem cells proliferation and myeloid cell differentiation remains poorly defined. Here we report an unexpected pathogenic role for interleukin-27 receptor (IL-27R) in AAA development as genetic inactivation of IL-27R protected mice from AAA induced by Angiotensin (Ang) II. The mitigation of AAA in IL-27R deficient mice is associated with a blunted accumulation of myeloid cells in suprarenal aortas due to the surprising attenuation of Ang II-induced expansion of HSCs. The loss of IL-27R engages transcriptional programs that promote HSCs quiescence and suppresses myeloid lineage differentiation, decreasing mature cell production and myeloid cell accumulation in the aorta.We, therefore, illuminate how a prominent vascular disease can be distantly driven by cytokine dependent regulation of the bone marrow precursors.
Cognate epitope recognition by bovine CD4 and CD8 T cells is essential for primary expansion of antigen-specific cytotoxic T-cells following ex vivo stimulation with a candidateMycobacterium avium subsp. paratuberculosispeptide vaccine
Authors: Abdellrazeq Gaber S. , Fry Lindsay M. , Elnaggar Mahmoud M. , Bannantine John P. , Schneider David A. , Chamberlin William M. , Mahmoud Asmaa H. A. , Park Kun-Taek , Hulubei Victoria , Davis William C. 
Published: February 2019

AbstractStudies in cattle show CD8 cytotoxic T cells (CTL), with the ability to kill intracellular bacteria, develop following stimulation of monocyte-depleted peripheral blood mononuclear cells (mdPBMC) with conventional dendritic cells (cDC) and monocyte-derived DC (MoDC) pulsed with MMP, a membrane protein fromMycobacterium aviumsubsp.paratuberculosis(Map) encoded byMAP2121c. CTL activity was diminished if CD4 T cells were depleted from mdPBMC before antigen (Ag) presentation by cDC and MoDC, suggesting simultaneous cognate recognition of MMP epitopes presented by MHC I and MHC II molecules might be essential for development of CTL activity. To clarify whether cognate recognition is essential for CTL development, studies were conducted with mdPBMC cultures in the presence of monoclonal antibodies (mAbs) specific for MHC class I and MHC class II molecules. The CTL response of mdPBMC to MMP-pulsed DC was completely blocked in the presence of mAbs to both MHC I and II molecules and also blocked in the presence of mAbs to either MHC I or MHC II. The results demonstrate CD4 T-cell help is essential for development of a primary CTL response to MMP, and indicate that cognate recognition is required for delivery of CD4 T-cell help during priming. Of importance, the findings provide support for the importance of CD4 and CD8 T-cell cognate antigen recognition in eliciting CTL responses to vaccines against intracellular pathogens. The methods described herein can be used to elucidate the intracellular interactions between lymphocytes and DC in humans and cattle.
Corrosion behavior of X65 pipeline steel in coastal areas
Authors: Sun BaoZhuang , Liao Wenju , Li Zhong , Liu Zhiyong , Du Cuiwei 
Published: February 2019

Purpose
To study the corrosion behavior of pipeline steel in coastal areas, a tidal seawater macro-cell corrosion device was built using a cycle soaking tank and a macro-cell corrosion facility to simulate the corrosion behavior of pipeline steel in a simulated coastal environment (dry and wet alternations during seawater-soil corrosion macro-cell processes).

Design/methodology/approach
The corrosion behaviors were studied via the weight loss method, electrochemical methods and morphological observations on corrosion.

Findings
The results show that during the initial stage of tidal seawater/soil macro-cell corrosion process of the X65 steel, the working electrode on the seawater side is the anode of the macro-battery. As corrosion progresses, the anode and the cathode of the macro-battery become inverted. As the area ratio and the dry – wet ratio increase, the time of anode and cathode inversion shortens. Galvanic current density decreases as the dry – wet ratio increases and increases as the area ratio increases. The corrosion process of macro-cell is affected by the reversal of anode and cathode. After the reversal of anode and cathode, the corrosion rate is mainly controlled by dry – wet alternating corrosion.

Originality/value
The corrosion behavior of a pipeline steel in a coastal environment was studied using a tidal seawater macro-cell corrosion device. The synergism effect between the tidal seawater and seawater-soil macro-cell on corrosion behavior was clarified.
Effect of diffusion alloying time on corrosion resistance and surface conductivity of niobium-alloying-modified AISI430 stainless steel for DFAFC bipolar plate
Authors: Han Jixin , Zhang Haibang , Sun Juncai , Zhao Wenyuan , Cui Jinlong 
Published: February 2019

PurposeThe purpose of this study is to improve the surface electrical conductivity and corrosion resistance of AISI430 stainless steel (430 SS) as bipolar plates for direct formic acid fuel cell (DFAFC).Design/methodology/approachThe niobium diffusion layers have been successfully synthesized on 430 SS substrate by the plasma surface diffusion alloying technique under different diffusion alloying time.FindingsThe surface morphology of Nb-modified 430 SS prepared under the diffusion alloying time of 2 h is more homogeneous, relatively sleek and compact without surface micropore and other common surface blemishes. The potentiostatic and potentiodynamic polarization measurements manifest that Nb-modified 430 SS prepared under the diffusion alloying time of 2 h enormously ameliorate the corrosion resistance of bare 430 SS compared with other Nb-modified 430 SS samples and its corrosion current density is maintained at −1.4 µA cm−2in simulated anodic environment of DFAFC (0.05 M H2SO4+ 2 ppm HF + 10 M formic acid at 50 °C).Originality/valueThe effect of diffusion alloying time on the corrosion resistance and surface conductivity of Nb-modified 430 SS has been carefully studied. The Nb-modified 430 SS samples prepared at the diffusion alloying time of 2 h have the best surface electrical conductivity and corrosion resistance in the simulated anodic environment of DFAFC.
Circumscribed interests in autism: are there sex differences?
Authors: Nowell Sallie Wallace , Jones Desiree R. , Harrop Clare 
Published: February 2019

Purpose
Sex differences in circumscribed interests (CI) may delay diagnosis for females with autism spectrum disorder (ASD); therefore, it is important to characterize sex differences in CI to determine if differential approaches to diagnostic assessment are warranted for females with ASD. The purpose of this paper is to examine sex differences in parent-reported quantity, content and functional impairment of children’s interests.

Design/methodology/approach
Parent responses to the Interests Scale were analyzed using descriptive statistics and ANOVAs to determine diagnostic (ASD vs typical development (TD)) and sex differences between four groups of children ages six to ten years: ASD males, ASD females, TD males and TD females.

Findings
Groups were comparable on the quantity of interests reported on the Interests Scale. Children with ASD demonstrated significantly more nonsocial interests and had greater functional impairment associated with their interests than TD children. A significant diagnosis×sex effect was found for the number of interests in folk psychology. Descriptively, males with ASD were more likely to have a primary interest in the traditionally male category of physics than females with ASD whose primary interest mainly fell into the categories of TV or the more traditionally female category of psychology.

Originality/value
These findings strengthen the results of Turner-Brown et al. (2011) by replicating their findings that children with ASD have more nonsocial interests and greater functional impairments related to their interests compared to TD children in a sample that is balanced on biological sex. However, there are distinctions between males and females with ASD in their primary interests that have implications for diagnostic assessment.