Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-genome sequencing of 128 camels across Asia provides insights into origin and migration of domestic Bactrian camels

The domestic Bactrian camels were treated as the principal means of locomotion between the eastern and western cultures in history. To address the question of their origin, we performed whole-genome sequencing of 128 camels across Asia, including representative populations of domestic Bactrian camels from the Mongolian Plateau to the Caspian Sea, as well as the extant wild Bactrian camels and dromedaries. The domestic and wild Bactrian camels showed remarkable genetic divergence since they were split from dromedaries, confirming they were separated species. The wild Bactrian camels made also little contribution to the ancestry of domestic ones. Among the domestic Bactrian camels, those from Iran exhibited the largest genetic distance from others, and were the first population to separate in the phylogeny. Although evident admixture was observed between domestic Bactrian camels and dromedaries living around the Caspian Sea, the large genetic distance and basal position of Iranian Bactrian camels could not be explained by introgression alone. Taken together, our study favored the Iranian origin of domestic Bactrian camels, which were then immigrated eastward to Mongolia where the native wild Bactrian camels inhabited. This study illustrated the complex genomic landscape of migration underlying domestication in Bactrian camels.
Atezolizumab potentiates Tcell-mediated cytotoxicity and coordinates with FAK to suppress cell invasion and motility in PD-L1+ triple negative breast cancer cells

ABSTRACT Immune check point inhibitors targeting programmed cell death protein-1 (PD-1) and its ligand (PD-L1) have shown clinical success in treatment of human malignancies. Triple negative breast cancer (TNBC), which is primarily characterized by high heterogeneity and presence of tumor infiltrating lymphocytes, remains therapeutic challenge due to unavailability of approved targeted therapy. Therapeutic potential of immune check point inhibitors for TNBC patients is under active clinical investigation. In this study, we show that FDA-approved anti-PD-L1 antibody, atezolizumab (ATE), potentiates T cell-mediated cytotoxicity and apoptosis of TNBC cells that express higher levels of PD-L1, but does not have significant effect on TNBC cells expressing low levels of PD-L1. PD-L1 knockdown further confirmed that ability of ATE to promote T cell-induced cytotoxicity is PD-L1 expression dependent. Combination of ATE with PD-L1 upregulating agents, such as HDAC, proteasomal, and lysosomal inhibitors, further augmented cytotoxic activity of T cells toward TNBC cells. Based on analysis of breast cancer tissue samples deposited in The Cancer Genome Atlas (TCGA), we found a positive correlation between PD-L1 and focal adhesion kinase (FAK) mRNA expression in PD-L1-positive (PD-L1+) TNBC, suggesting a functional association of FAK and immune checkpoints. We further demonstrate that ATE dramatically downregulates phosphorylation status of FAK, an important regulator of cell invasion and migration, and significantly enhances FAK inhibitor mediated inhibition of cell motility and invasion of PD-L1+ TNBC cells independent of T cells. Taken together, our data suggest that ATE shows promising anti-tumor activity in PD-L1+ TNBC via both T cell-dependent and -independent mechanisms.
PERIOPERATIVE PROCESS AND OUTCOME INDICATORS FOR PANCREATIC DUCTAL ADENOCARCINOMA IN A TERTIARY CARE INSTITUTION: A DESCRIPTIVE STUDY

vi List of Abbreviations Used . vii Chapter 1: Introduction . 1 Chapter 2: Literature Review . 3 2.1 Pancreatic Ductal Adenocarcinoma Epidemiology and Risk Factors . 3 2.1. 1 Epidemiology and Risk Factors . 3 2.1. 2 Future Estimates of PDAC . 4 2.2 Pancreatic Ductal Adenocarcinoma Presentation and Natural History . 4 2.3 Pancreatic adenocarcinoma screening and diagnosis. 6 2.4 Advances in Pancreatic Ductal Adenocarcinoma Treatment and Healthcare Delivery . 7 2.4.1 Pancreatic Ductal Adenocarcinoma Surgical Treatment Advances . 8 2.4.2 Pancreatic Ductal Adenocarcinoma Adjuvant Treatment Advances . 8 2.4.3 Pancreatic Ductal Adenocarcinoma Advances in Healthcare Delivery . 9 2.4.4 The Impact of Pathology Techniques and Reporting on Prognostication for Pancreatic Ductal Adenocarcinoma Patients . 11 2.4.5 Variation in Pancreatic Ductal Adenocarcinoma Outcomes in Canada . 13 2.6 Quality in Pancreatic Ductal Adenocarcinoma Treatment. 14 2.6. 1 Process and Outcome Quality Indicators . 15 Chapter 3: Objectives . 24 Chapter 4: Methods. 25 4.1 Study Design and Overview . 25 4.2 Population and Patient Selection . 26 4.3 Data Sources . 28 4.3. 1 Chart Review. 28 4.3. 2 Description and Quality of Data Sources . 28 4.4 Data Linkage . 30 4.5 Study Variables . 31 4.5. 1 Demographic and Clinical Characteristics . 32 4.5. 2 Tumor-related variables . 32 4.5. 3 Processes of Care . 32 4.5. 4 Shortand Long-Term Outcomes . 34
HRM, Trust in Employer and Organizational Performance

This paper draws upon social exchange theory to examine the explanatory power of employees' trust in their employer as the mediating variable between an organization's human resources (HR) management interventions and performance outcomes at individual, work unit and organizational levels. We utilize two large-scale survey studies in two different organizations, from the forestry and information and communications technology (ICT) industries in Finland: a forest company (411 respondents) and an ICT company (304 respondents) were analysed with confirmatory factor analysis and structural equation modelling. The results for the two studies validated all our hypotheses including the mediating role of trust in employer. The results do suggest that if HR management can be designed specifically to enhance employees' trust in their organization, its effect on performance is positive. In a practical point of view, our findings provide new insights into the nature of organizational trust, and particularly the impersonal dimension for practitioners, especially those in HR. The evidence from two studies is that HR policies can enhance employees' trust towards their employer and, through this, the performance of the organization. Copyright © 2015 John Wiley & Sons, Ltd.
A Novel Feature Extraction Model Using Learnable Evolution Model

In this paper, we presents a new classification algorithm called( LEM+ID3) and extending our previous work, which is based on the techniques from the learnable evolution models (LEM) to improve convergence and accuracy of the algorithm and use of ID3 in order to construct the tree used in classification. We converted LEM from optimization domain to classification domain and then examine the feature extraction problems and show that learning evolutional can significantly enhance the performance of pattern recognition systems with simple classifiers. We have applied this model to real world datasets from the UCI Machine Learning databases to verify our approach and compare our proposed approach with other reported results. We conclude that our algorithm is able to produce classifiers of superior (or equivalent) performance to the conventional classifiers examined.
The Effect of Reproductive Factors on Coronary Artery Disease in Women

Abstract Introduction: There is a sex discrepancy in cardiovascular physiology. In this study, we aimed to investigate the effect of female reproductive factors on coronary artery disease (CAD) beyond the known CAD risk factors. Methods: In a case-control study, women referred to Tehran Heart Center for coronary artery angiography from 2012 to 2014 were enrolled. Of these, 80 premenopausal and 100 postmenopausal females with CAD in angiography were randomly selected as cases and 80 premenopausal and 100 postmenopausal females without CAD in angiography were selected as controls. A questionnaire including reproductive history and known CAD risk factors was filled for every subject. Analysis was performed separately for pre and postmenopausal women and a final adjustment for coronary artery disease risk factors was done. Results: Among reproductive factors, oligomenorrhea (OR= 6.72) was a significant risk factor for CAD in premenopausal women and history of oral contraceptive (OCP) use had a protective effect on CAD in pre and postmenopausal woman (OR= 0.24 and 0.20, respectively). Conclusions: Since oligomenorrhea has a strong association with insulin resistance and diabetes, a conventional risk factor of CAD, women with oligomenorrhea should be treated not only for cyclic irregularity but also for prevention of CAD.
Petunia- and Arabidopsis-Specific Root Microbiota Responses to Phosphate Supplementation

Phosphorus (P) is a limiting element for plant growth. Several root microbes, including arbuscular mycorrhizal fungi (AMF), have the capacity to improve plant nutrition and their abundance is known to depend on P fertility. However, how complex root-associated bacterial and fungal communities respond to various levels of P supplementation remains ill-defined. Here we investigated the responses of the root-associated bacteria and fungi to varying levels of P supply using 16S rRNA gene and internal transcribed spacer amplicon sequencing. We grew Petunia, which forms symbiosis with AMF, and the nonmycorrhizal model species Arabidopsis as a control in a soil that is limiting in plant-available P and we then supplemented the plants with complete fertilizer solutions that varied only in their phosphate concentrations. We searched for microbes, whose abundances varied by P fertilization, tested whether a core microbiota responding to the P treatments could be identified and asked whether bacterial and fungal co-occurrence patterns change in response to the varying P levels. Root microbiota composition varied substantially in response to the varying P application. A core microbiota was not identified as different bacterial and fungal groups responded to low-P conditions in Arabidopsis and Petunia. Microbes with P-dependent abundance patterns included Mortierellomycotina in Arabidopsis, while in Petunia, they included AMF and their symbiotic endobacteria. Of note, the P-dependent root colonization by AMF was reliably quantified by sequencing. The fact that the root microbiotas of the two plant species responded differently to low-P conditions suggests that plant species specificity would need to be considered for the eventual development of microbial products that improve plant P nutrition. [Formula: see text]Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Post-retrieval Extinction Prevents Reconsolidation of Methamphetamine Memory Traces and Subsequent Reinstatement of Methamphetamine Seeking

Methamphetamine abuse has become a serious public health problem. However, effective treatment for methamphetamine addiction remains elusive, especially considering its high rate of relapse after treatment. A conditioned stimulus (CS) memory retrieval–extinction procedure has been demonstrated to decrease reinstatement of cocaine, heroin, and alcohol seeking in rats, and to reduce cue-induced cravings in heroin and nicotine addicts. The goal of the present study is to explore the effect of the CS memory retrieval–extinction procedure on methamphetamine seeking in rats and the underlying mechanisms. We found that daily retrieval of methamphetamine-associated memories 1 h before extinction sessions decreased subsequent drug priming-induced reinstatement, spontaneous recovery, and renewal of methamphetamine seeking. We also found that retrieval of methamphetamine-associated memories induced neuronal activation in the basolateral amygdala (BLA), while presenting extinction within the time window of reconsolidation abolished the neuronal activation in BLA. These results indicate that the CS memory retrieval–extinction procedure could prevent reconsolidation of methamphetamine memory traces in BLA and subsequent methamphetamine craving and relapse.
Role of the NMDA receptor subunit, NR3A, in glutamatergic synapse development

Subunit composition of NMDA-type glutamate receptors (NMDARs) dictates their function, yet the ontogenic profiles of human NMDAR subunits from gestation to adulthood have not been determined. We examined NMDAR mRNA and protein development in human dorsolateral prefrontal cortex (DLPFC), an area in which NMDARs are critical for higher cognitive processing and NMDAR hypofunction is hypothesized in schizophrenia. Using quantitative RT-PCR and western blotting, we found NR1 expression begins low prenatally, peaks in adolescence, yet remains high throughout life, suggesting lifelong importance of NMDAR function. In contrast, NR3A levels are low during gestation, surge soon after birth, and decline progressively through adolescence and into adulthood. Because NR3A subunits uniquely attenuate NMDARmediated currents, limit calcium influx, and suppress dendritic spine formation, high levels during early childhood may be important for regulating neuroprotection and activity-dependent sculpting of synapses. We also examined whether subunit changes underlie reduced NMDAR activity in schizophrenia. Our results reveal normal NR1 and NR3A protein levels in DLPFC from schizophrenic patients, indicating that NMDAR hypofunction is unlikely to be maintained by gross changes in NR3A-containing NMDARs or overall NMDAR numbers. These data provide insights into NMDAR
Micromechanical Investigation of Stress Relaxation in Gas Hydrate-Bearing Sediments Due to Sand Production

Past experience of gas production from methane-hydrate-bearing sediments indicates that sand migration is a major factor restricting the production of gas from methane-hydrate reservoirs. One important geotechnical aspect of sand migration is the influence of grain detachment on the existing stresses. This paper focuses on understanding and quantifying the nature of this aspect using different approaches, with a focus on discrete element method (DEM) simulations of sand detachment from hydrate-bearing sand samples. The investigation in the paper reveals that sand migration affects isotropic and deviatoric stresses differently. In addition, the existence of hydrate moderates the magnitude of stress relaxation. Both of these features are currently missing from continuum-based models, and therefore, a new constitutive model for stress relaxation is suggested, incorporating the research findings. Model parameters are suggested based on the DEM simulations. The model is suitable for continuum mechanics-based simulations of gas production from hydrate reservoirs.
STATISTICAL BROADBAND OVER POWER LINES CHANNEL MODELING - PART 2: THE NUMERICAL RESULTS OF THE STATISTICAL HYBRID MODEL

This second paper presents the numerical evaluation of the statistical hybrid model for a number of indicative overhead medium-voltage (OV MV) and underground medium-voltage (UN MV) broadband over power lines (BPL) topologies. In essence, this paper assesses the effect of a number of key factors already reported in [1], such as the distribution power grid type, BPL topology class, coupling scheme, channel attenuation statistical distribution, and injected power spectral density (IPSD) limits, on the computed capacity ranges of the statistical hybrid model. For the assessment of the different channel attenuation statistical distributions, the graphical analysis and the proposed metrics of capacity percentage change and average absolute capacity percentage change are demonstrated while two rules of thumb estimating the fidelity results are also proposed.
POTENCY OF OIL SLUDGE INDIGENOUS BACTERIA FROM DUMAI-RIAU IN PRODUCING BIOSURFACTANT ON VARIATION OF SACCHARIDE SUBSTRATES

This study aims to detect the ability of four species of Dumai-Riau oil sludge indigenous bacteria to produce biosurfactants using 3 types of substrate (D-glucose, sucrose and molasses) and to determine the relationship between the five biosurfactant detection methods. The bacteria were grown on liquid mineral medium with addition of 2% saccharide substrates. The culture was incubated for 4 days at 300C. Production of biosurfactants by bacteria is detected in various ways by indirectly evaluating the presence of biosurfactant in the culture supernatant by measuring the surface tension (mN / m), emulsification (%), oil spreading, drop collapse and knowing the bacteria's ability to lysis blood agar media. The study used a completely randomized design with 4 treatments and 3 replications. The data were analyzed descriptively and statistically using Anova and continued with Duncan test and Pearson correlation test was performed to test the correlation between methods. The results showed the four bacteria gave different growth responses when grown on different substrates. The ability of bacteria to produce biosurfactants also varies depending on the type of substrates. The result of surface tension method has correlation with result of oil spreading method, blood agar test and emulsification activity.
The Development of the Human Adaptive Immune System and Its Role in Promoting Immunological Tolerance

Author(s): Mold, Jeffrey Eron | Advisor(s): McCune, Joseph M. | Abstract: The developing immune system has long been recognized to be uniquely prone to tolerance induction. Historical observations in rodent models, suggest that the tolerogenic properties of the fetus and neonate are linked to the immaturity of the adaptive immune system at this stage of development. However, the adaptive immune system of larger mammals undergoes considerable maturation during fetal development and is not thought to be amenable to tolerance induction at this time. There have, however, been clinical observations that suggest that the human fetus may be subject to tolerance induction under certain conditions, though very little is known about the mechanisms underlying such tolerance. This is in part attributable to a general deficit of knowledge concerning the functional properties of the developing immune system in human beings. We characterized fetal T cells at early stages of T cell development (10-20 gestational weeks (g.w.)). Our analysis revealed that a high frequency of fetal CD4+ T cells bore the phenotype of regulatory T cells (TReg). Analysis of neonatal cord blood and adult peripheral blood and lymphoid tissues revealed that fetal tissues contained greater frequencies of TReg than neonates or adults. These observations, coupled with the clinical findings that certain individuals showed tolerance to non-inherited maternal HLA molecules in a transplant setting, led to the hypothesis that fetal TReg could play a role in suppressing T cell responses to maternal alloantigens. A survey of lymph node specimens revealed that maternal cells could be detected within the developing fetal tissues. Fetal T cells were highly responsive to alloantigens yet fetal TReg were capable of suppressing fetal T cell responses to maternal alloantigens. Stimulation of naive fetal T cells with alloantigens led to the differentiation and expansion of TReg cells, providing a mechanism for how tolerance could be achieved following fetal exposure to foreign antigens in humans. Ongoing studies have revealed that the tolerogenic properties of the developing fetal immune system may be rooted in changes that occur within the hematopoietic stem cell (HSC) compartment. These findings provide novel insights into the development of immunological tolerance in human beings.
Immune microenvironment profiling of gastrointestinal stromal tumors (GIST) shows gene expression patterns associated to immune checkpoint inhibitors response

ABSTRACT Few studies were conducted investigating the immunological profiles in gastrointestinal stromal tumors (GIST). Adaptive and innate immune cells are present in the tumor microenvironment, indicating GIST as inflamed tumors. In addition, murine models suggested a potential interaction between immune components and imatinib. In this retrospective study, the GIST immunological profile was investigated through in silico analysis and immunohistochemistry (IHC), exploring the basis for immunotherapy approaches. Gene expression profiles (GEP) from 31 KIT/PDGFRA-mutant GIST were analyzed to evaluate the tumor microenvironment and immunotherapy predictive signatures such as the expanded IFN-γ-induced immune signature (EIIS) and the T-cell-inflamed signature (TIS). GEP and IHC supported the presence of immune infiltrate in GIST, with dominance of CD4+ and CD8+ T cells and M2 macrophages showing a remarkable similarity with melanoma microenvironment. The EIIS genes were expressed in most of GIST samples and positively correlated with PD-L1 abundance (p < .0001). Co-expression was also found between PD-L1 and CD8A (p < .0001) or CD8B (p = .0003). Moreover, the median TIS score for GIST was between the 65th and 70th percentile of the Cancer Genome Atlas dataset, in the same range of tumors responding to anti-PD-1/PD-L1. Analysis of the Gene Expression Omnibus database GIST samples pre- and post-treatment confirmed that imatinib downregulates PD-L1 and IRF1 expression through the inhibition of KIT and PDGFRA, thus contributing to counteract the suppressed adaptive immune response against GIST. The presence of a rich immune infiltrate in GIST along with the presence of TIS and EIIS suggests that GIST may benefit from immunotherapy along with tyrosine kinase inhibitors.
Novel fishway entrance modifications for Pacific lamprey

Abstract Passage facilities at dams must accommodate a broad array of aquatic species to achieve full river connectivity. In an attempt to improve adult Pacific lamprey (Entosphenus tridentatus) passage, fishway entrance modifications were made at a large dam on the Columbia River in northwestern USA. The modifications consisted of a variable-width entrance weir and flow disrupters to create heterogeneity in water velocities near the bottom, without affecting attraction flows for adult salmonids (Oncorhynchus spp.) or alosids (Alosa sapidissima). Additionally, a lamprey passage structure (LPS) was installed to provide a lamprey-specific route from tailrace to forebay elevation (31 m). Passive integrated transponders and radio transmitters were used to monitor both Pacific lamprey and Chinook salmon (O. tshawytscha) movements. Fish use of the modified entrance was compared to that at a similar, but unmodified entrance before and after modifications. The entrance modifications resulted in increased velocity heterogeneity, but no measurable improvement in entrance efficiencies for lamprey or salmon. Lamprey successfully ascended the LPS, with annual counts ranging from 48 in 2010 to 3,851 in 2016 (0.2–8.9% of lamprey counted at the dam). Radiotelemetry indicated that tagged lamprey resumed upstream passage after LPS use and travelled at rates similar to those that used traditional fishway routes.
Integrating Multimedia ICT Software in Language Curriculum: Students’ Perception, Use, and Effectivenes

Information and Communication Technologies (ICT) constitute an integral part of the teaching and learning environment in present-day educational institutions and play an increasingly important role in the modern second language classroom. In this study, an online language learning tool Tell Me More (TMM) has been introduced as a supplementary tool in French and German first and second-year language university classes. At the end of the academic year, the students completed a questionnaire exploring their TMM usage behaviour and perception of the software. The survey also addressed aspects of the respondents' readiness for self-directed language learning. The data were then imported into SPSS and underwent statistical analysis. The results of the study show that 1) relatively few of today's university students are open to the idea of voluntarily using ICT for independent language practice; 2) grade, price, and availability of alternative means of language practice are the most important factors affecting the students' decision to purchase and use ICT software; 3) there is a relationship between the students' decision to buy and use ICT software and their readiness for self-directed learning.