Miracle-dz/UniFAR-FTUs huggingface dataset:
EXPERIMENTAL INFECTION OF NONTARGET SPECIES OF RODENTS AND BIRDS WITH BRUCELLA ABORTUS STRAIN RB51 VACCINE

The Brucella abortus vaccine strain RB51 (SRB51) is being considered for use in the management of brucellosis in wild bison (Bison bison) and elk (Cervus elaphus) populations in the Greater Yellowstone Area (USA). Evaluation of the vaccine's safety in non-target species was considered necessary prior to field use. Between June 1998 and December 1999, ground squirrels (Spermophilus richardsonii, n = 21), deer mice (Peromyscus maniculatus, n = 14), prairie voles (Microtus ochrogaster, n = 21), and ravens (Corvus corax, n = 13) were orally inoculated with SRB51 or physiologic saline. Oral and rectal swabs and blood samples were collected for bacteriologic evaluation. Rodents were necropsied at 8 to 10 wk and 12 to 21 wk post inoculation (PI), and ravens at 7 and 11 wk PI. Spleen, liver and reproductive tissues were collected for bacteriologic and histopathologic evaluation. No differences in clinical signs, appetite, weight loss or gain, or activity were observed between saline- and SRB51-inoculated animals in all four species. Oral and rectal swabs from all species were negative throughout the study. In tissues obtained from SRB51-inoculated animals, the organism was isolated from six of seven (86%) ground squirrels, one of six (17%) deer mice, none of seven voles, and one of five (20%) ravens necropsied at 8, 8, 10, and 7 wk PI, respectively. Tissues from four of seven (57%) SRB51-inoculated ground squirrels were culture positive for the organism 12 wk PI; SRB51 was not recovered from deer mice, voles, or ravens necropsied 12, 21, or 11 wk, respectively, PI. SRB51 was not recovered from saline-inoculated ground squirrels, deer mice, or voles at any time but was recovered from one saline-inoculated raven at necropsy, 7 wk PI, likely attributable to contact with SRB51-inoculated ravens in an adjacent aviary room. Spleen was the primary tissue site of colonization in ground squirrels, followed by the liver and reproductive organs. The results indicate oral exposure to SRB51 does not produce morbibity or mortality in ravens, ground squirrels, deer mice, or prairie voles.
Does aquaculture add resilience to the global food system?

Aquaculture is the fastest growing food sector and continues to expand alongside terrestrial crop and livestock production. Using portfolio theory as a conceptual framework, we explore how current interconnections between the aquaculture, crop, livestock, and fisheries sectors act as an impediment to, or an opportunity for, enhanced resilience in the global food system given increased resource scarcity and climate change. Aquaculture can potentially enhance resilience through improved resource use efficiencies and increased diversification of farmed species, locales of production, and feeding strategies. However, aquaculture’s reliance on terrestrial crops and wild fish for feeds, its dependence on freshwater and land for culture sites, and its broad array of environmental impacts diminishes its ability to add resilience. Feeds for livestock and farmed fish that are fed rely largely on the same crops, although the fraction destined for aquaculture is presently small (∼4%). As demand for high-value fed aquaculture products grows, competition for these crops will also rise, as will the demand for wild fish as feed inputs. Many of these crops and forage fish are also consumed directly by humans and provide essential nutrition for low-income households. Their rising use in aquafeeds has the potential to increase price levels and volatility, worsening food insecurity among the most vulnerable populations. Although the diversification of global food production systems that includes aquaculture offers promise for enhanced resilience, such promise will not be realized if government policies fail to provide adequate incentives for resource efficiency, equity, and environmental protection.
Compartmentalization of HIV-1 in the central nervous system: role of the choroid plexus

Objectives:To determine the genetic and phenotypic composition of HIV-1 found in the choroid plexus (CPx) and its relationship to virus in the brain and peripheral lymphoid tissue. Design:Phenotypic and molecular comparisons of HIV-1 found in autopsy brain, CPx, and spleen tissues. Methods:HIV-1 was co-cultured from matched postmortem brain (basal ganglia), CPx, and spleen tissues of AIDS patients with and without HIV-associated encephalitis and dementia. Viral phenotypes were determined by infection of monocyte-derived macrophages, MT-2 or co-receptor-specific cell lines. Viral env and pol sequences were determined from genomic DNA isolated directly from tissues or co-cultures, and phylogenetic comparisons were performed. Results:CCR5-utilization was the most prevalent viral tropism found in all tissues, although spleen isolates also displayed CXCR4 usage. Viruses isolated from CPx consisted of both peripheral and brain-like virus, but were more related phenotypically and genetically to those found in the brain. Mutations found in the pol gene that could confer drug resistance to brain and CPx isolates were similar to those found in the periphery. Conclusion:The CPx contained replication-competent virus that was most similar, although distinct, from that found in the brain. It also contained some viruses with high similarity to those of peripheral origin. Compartmentalization of viral env and pol sequences indicated that differential selective pressures exist in each tissue examined. These studies suggest that the CPx may provide an environment that promotes the evolution of drug-resistant strains with central nervous system tropism, although it is unlikely to be a reservoir for archival HIV-1 variants.
Longer Retention Time of Fluoridated Varnishes Enhances Enamel Remineralisation In Vitro.

PURPOSE Widely used in caries prevention, fluoridated varnish (FV) is also capable of remineralising carious lesions. However, the retention time of FV needed on enamel to ensure the maximum benefit is unclear. This study aimed to determine whether an increase in the retention time of 5% sodium fluoride (NaF) varnishes on enamel carious lesions enhances remineralisation. MATERIALS AND METHODS Carious lesions were generated on bovine enamel slabs and treated with one of three 5% NaF commercial varnishes: Duraphat, Durashield or FlorOpal. After application, the varnishes were maintained on the slabs for 8, 12, 18, 24, 36 or 48 h while immersed in artificial saliva. Remineralisation efficacy was calculated and expressed as the percentage of surface microhardness recovery (%SHR). Untreated carious lesions served as negative controls. Data from each timepoint for each product were compared by ANOVA, followed by a post-hoc test (p < 0.05). RESULTS There was a trend for increased remineralisation over time, reaching maximum %SHR values of about 30% after 18 to 24 h. No significant differences were detected after 18 h (p > 0.05). This remineralisation dynamic was similar among the three tested products. CONCLUSION Remineralisation of enamel lesions using 5% NaF varnish appears to be initially dependent on the retention time of the product. Higher remineralisation was observed upon 18 h of varnish retention on the lesions.
Expression Signature of MicroRNA-155 and its Association with Response to Treatment within Different Subtypes of B-Cell Malignancies

Objectives: Emerging evidence suggests that microRNAs could serve as non-invasive biomarkers for cancer patients. However, they are mostly not fully investigated as biomarkers in the classification, progression and prognosis of different cancers. Our study was designed to explore the microRNA-155 (miR-155) expression levels in peripheral blood mononuclear cells (PBMCs) in patients with various subtypes of B-cell malignancies. Also, we aimed to correlate between miR-155 expression levels and the diverse clinico-pathologic features as well as the prognostic fate of these patients after treatment completion. Subjects and methods: Using whole blood samples from 53 patients with B-cell malignancies and 15 apparently healthy subjects, miR-155 was extracted and profiled by quantitative real-time PCR (RT-qPCR). The B-cell malignancies patients were including 22 diffuse large B-cell lymphoma (DLBCL), 15 chronic lymphocytic leukemia (CLL), 9 follicular lymphoma patients (FL) and 7 subjects with burkitt′s lymphoma (BL). The samples were withdrawn before starting chemotherapy in addition to after completing their therapeutic courses by 6 months. Subsequently, the patients were further sub-grouped into those with partial remission, complete remission, resistant disease and relapse. Results: We found that miR-155 expression levels differentiate lymphoma entities from normal subjects (p ≤ 0.001) and its expression fold changes distinguish B-cell lymphoma subtypes from each other’s (p<0.05). In addition, miR-155 was significantly correlated with age and LDH levels. The receiver operating curve (ROC) was employed to identify the diagnostic outcomes of miR-155 in discriminating B-cell malignancies entities from each other’s (AUC=0.957 for DLBCL vs. CLL+FL and AUC=1.000 for CLL vs. FL). Otherwise, when BL was versus healthy controls the AUC was equal to 0.552. As well, we demonstrated an association between elevated miR-155 expression levels and poor response to treatment with increased cases of relapse, partial remission or resistance to treatment. Conclusions: This study suggests that miR-155 has an expression profile that differs according to B-cell malignancies subtype. Besides, miR-155 expression levels may modulate the patient’s response to treatment. These results support a role for miR-155 to provide helpful diagnostic/prognostic information in B-cell malignancies and may highlight novel pathways to be targeted for therapeutics in the future.
CD34+ Cells Represent Highly Functional Endothelial Progenitor Cells in Murine Bone Marrow

Background Endothelial progenitor cells (EPCs) were shown to have angiogenic potential contributing to neovascularization. However, a clear definition of mouse EPCs by cell surface markers still remains elusive. We hypothesized that CD34 could be used for identification and isolation of functional EPCs from mouse bone marrow. Methodology/Principal Findings CD34+ cells, c-Kit+/Sca-1+/Lin− (KSL) cells, c-Kit+/Lin− (KL) cells and Sca-1+/Lin− (SL) cells were isolated from mouse bone marrow mononuclear cells (BMMNCs) using fluorescent activated cell sorting. EPC colony forming capacity and differentiation capacity into endothelial lineage were examined in the cells. Although CD34+ cells showed the lowest EPC colony forming activity, CD34+ cells exhibited under endothelial culture conditions a more adherent phenotype compared with the others, demonstrating the highest mRNA expression levels of endothelial markers vWF, VE-cadherin, and Flk-1. Furthermore, a dramatic increase in immediate recruitment of cells to the myocardium following myocardial infarction and systemic cell injection was observed for CD34+ cells comparing with others, which could be explained by the highest mRNA expression levels of key homing-related molecules Integrin β2 and CXCR4 in CD34+ cells. Cell retention and incorporation into the vasculature of the ischemic myocardium was also markedly increased in the CD34+ cell-injected group, giving a possible explanation for significant reduction in fibrosis area, significant increase in neovascularization and the best cardiac functional recovery in this group in comparison with the others. Conclusion These findings suggest that mouse CD34+ cells may represent a functional EPC population in bone marrow, which could benefit the investigation of therapeutic EPC biology.
Improving Verification Accuracy of CPS by Modeling and Calibrating Interaction Uncertainty

Cyber-Physical Systems (CPS) intrinsically combine hardware and physical systems with software and network, which are together creating complex and correlated interactions. CPS applications often experience uncertainty in interacting with environment through unreliable sensors. They can be faulty and exhibit runtime errors if developers have not considered environmental interaction uncertainty adequately. Existing work in verifying CPS applications ignores interaction uncertainty and thus may overlook uncertainty-related faults. To improve verification accuracy, in this article we propose a novel approach to verifying CPS applications with explicit modeling of uncertainty arisen in the interaction between them and the environment. Our approach builds an Interactive State Machine network for a CPS application and models interaction uncertainty by error ranges and distributions. Then it encodes both the application and uncertainty models to Satisfiability Modulo Theories (SMT) formula to leverage SMT solvers searching for counterexamples that represent application failures. The precision of uncertainty model can affect the verification results. However, it may be difficult to model interaction uncertainty precisely enough at the beginning, because of the uncontrollable noise of sensors and insufficient data sample size. To further improve the accuracy of the verification results, we propose an approach to identifying and calibrating imprecise uncertainty models. We exploit the inconsistency between the counterexamples’ estimate and actual occurrence probabilities to identify possible imprecision in uncertainty models, and the calibration of imprecise models is to minimize the inconsistency, which is reduced to a Search-Based Software Engineering problem. We experimentally evaluated our verification and calibration approaches with real-world CPS applications, and the experimental results confirmed their effectiveness and efficiency.
Who emphasizes and who blurs? Party strategies in multidimensional competition

Most studies of party competition consider the presentation of ambiguous positions a costly strategy. This literature, however, does not study party strategies in multiple issue dimensions. Yet multidimensionality may play an important role in parties’ strategic calculus. Although it may be rational for a party to emphasize a certain issue dimension, it may be equally rational to disguise its stance on other dimensions by blurring its position. This article argues that parties employ strategies of issue emphasis and position blurring in various dimensional contexts. Who emphasizes and who blurs thus depends on the actors’ relative stakes in different issue dimensions. The paper makes its case by performing cross-sectional analyses of 132 political parties in 14 West European party systems using Comparative Manifesto Project data, the 2006 Chapel Hill expert survey and the 2009 European Election Study.
DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields

Motivation Reconstructing the full-length expressed transcripts (a.k.a. the transcript assembly problem) from the short sequencing reads produced by RNA-seq protocol plays a central role in identifying novel genes and transcripts as well as in studying gene expressions and gene functions. A crucial step in transcript assembly is to accurately determine the splicing junctions and boundaries of the expressed transcripts from the reads alignment. In contrast to the splicing junctions that can be efficiently detected from spliced reads, the problem of identifying boundaries remains open and challenging, due to the fact that the signal related to boundaries is noisy and weak. Results We present DeepBound, an effective approach to identify boundaries of expressed transcripts from RNA-seq reads alignment. In its core DeepBound employs deep convolutional neural fields to learn the hidden distributions and patterns of boundaries. To accurately model the transition probabilities and to solve the label-imbalance problem, we novelly incorporate the AUC (area under the curve) score into the optimizing objective function. To address the issue that deep probabilistic graphical models requires large number of labeled training samples, we propose to use simulated RNA-seq datasets to train our model. Through extensive experimental studies on both simulation datasets of two species and biological datasets, we show that DeepBound consistently and significantly outperforms the two existing methods. Availability DeepBound is freely available at https://github.com/realbigws/DeepBound. Contact mingfu.shao@cs.cmu. edu, realbigws@gmail.com
WormBench: a configurable workload for evaluating transactional memory systems

Transactional Memory (TM) is a promising new technology that makes it possible to ease writing multi-threaded applications. Many different TM implementations exist, unfortunately most of those TM systems are currently evaluated by using workloads that are (1) tightly coupled to the interface of a particular TM implementation, (2) are small and lack to capture the common concurrency problems that exist in real multi-threaded applications and also (3) fail to evaluate the overall behavior of the Transactional Memory considering the complete software stack. WormBench is parameterized workload designed from the ground up to evaluate TM systems in terms of robustness and performance. Its goal is to provide an unified solution to the problems stated above (1, 2, 3). The critical sections in the code are marked with the atomic statements and thus proving a framework to test the compiler's ability to translate them properly and efficiently into the appropriate TM system interface. Its design considers the common synchronization problems that exist in TM multi-threaded applications. The behavior of WormBench can be changed by using run configurations which provide the ability to reproduce a runtime behavior observed in a typical multi-threaded application or a behavior that stresses a particular aspect of the TM system such as abort handling. In this paper, we analyze the transactional characteristics of WormBench by studying different run configurations and demonstrate how Worm-Bench can be configured to model the transactional behavior of an application from the STAMP benchmark suite.
Dynamics of martensitic structure at TiNb-based quenched alloys under heating and loading

Phase competition at TiNb-based Ni-free shape memory alloys caused by changes of alloying, temperature, external stresses is considered by analysis of experimental results on elastic modulus determination, X-ray diffraction, thermal analysis, mechanical tensile and indentation testing. Martensitic β↔α" transformation undergoes due to a reversible displacements of atoms at (002) plane of orthorhombic unit cell. The martensitic structure has high stability against thermal and mechanical cycling.
An energy balance criterion for nanoindentation-induced single and multiple dislocation events

Small volume deformation can produce two types of plastic instability events. The first involves dislocation nucleation as a dislocation by dislocation event and occurs in nanoparticles or bulk single crystals deformed by atomic force microscopy or small nanoindenter forces. For the second instability event, this involves larger scale nanocontacts into single crystals or their films wherein multiple dislocations cooperate to form a large displacement excursion or load drop. With dislocation work, surface work, and stored elastic energy, one can account for the energy expended in both single and multiple dislocation events. This leads to an energy balance criterion which can model both the displacement excursion and load drop in either constant load or fixed displacement experiments. Nanoindentation of Fe-3% Si (100) crystals with various oxide film thicknesses supports the proposed approach.
Application of Semantic Computing in Cancer on Secondary Data Analysis

There have been an enormous number of publications on cancer research. These integrated but unstructured cancer-related articles are of great value for cancer diagnosis, treatment and prevention. In this study, we use the basic concepts underlying text mining and semantic computing to discuss the current state-of-the-art text mining applications in cancer research. Using the abstract of literature extracted from PubMed between 2008 and 2016, a total 925,648 articles are used for subsequent text mining. Among the 925,648 articles, the top 5 most studied cancer types were breast cancer (23.82%), lung cancer (10.54%), prostate cancer (9.90%), rectal cancer (8.44%), and ovarian cancer (4.44%). The top 3 most frequently occurred keywords in the abstracts of the 925,648 articles are patients, cancer, and cell where each appear 1,445,688, 1,284,140, and 676,924 times, respectively. Analysis of the key concepts indicate that the most common concepts are patients, cancer, cell and tumor. Our results suggest that while the risk factors of cancer, treatment of cancer, and survival of cancer patients were popular research topics, end-of-life cancer care issues are less studied. Further studies should explore these areas since they are as important as treatment of the disease itself for many patients.
The Combinational Use of CRISPR/Cas9 and Targeted Toxin Technology Enables Efficient Isolation of Bi-Allelic Knockout Non-Human Mammalian Clones

Recent advances in genome editing systems such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease (CRISPR/Cas9) have facilitated genomic modification in mammalian cells. However, most systems employ transient treatment with selective drugs such as puromycin to obtain the desired genome-edited cells, which often allows some untransfected cells to survive and decreases the efficiency of generating genome-edited cells. Here, we developed a novel targeted toxin-based drug-free selection system for the enrichment of genome-edited cells. Cells were transfected with three expression vectors, each of which carries a guide RNA (gRNA), humanized Cas9 (hCas9) gene, or Clostridium perfringens-derived endo-β-galactosidase C (EndoGalC) gene. Once EndoGalC is expressed in a cell, it digests the cell-surface α-Gal epitope, which is specifically recognized by BS-I-B4 lectin (IB4). Three days after transfection, these cells were treated with cytotoxin saporin-conjugated IB4 (IB4SAP) for 30 min at 37 °C prior to cultivation in a normal medium. Untransfected cells and those weakly expressing EndoGalC will die due to the internalization of saporin. Cells transiently expressing EndoGalC strongly survive, and some of these surviving clones are expected to be genome-edited bi-allelic knockout (KO) clones due to their strong co-expression of gRNA and hCas9. When porcine α-1,3-galactosyltransferase gene, which can synthesize the α-Gal epitope, was attempted to be knocked out, 16.7% and 36.7% of the surviving clones were bi-allelic and mono-allelic knockout (KO) cells, respectively, which was in contrast to the isolation of clones in the absence of IB4SAP treatment. Namely, 0% and 13.3% of the resulting clones were bi-allelic and mono-allelic KO cells, respectively. A similar tendency was seen when other target genes such as DiGeorge syndrome critical region gene 2 and transforming growth factor-β receptor type 1 gene were targeted to be knocked out. Our results indicate that a combination of the CRISPR/Cas9 system and targeted toxin technology using IB4SAP allows efficient enrichment of genome-edited clones, particularly bi-allelic KO clones.