Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of the Relative Sensitivity of the Comparative Tuberculin Skin Test in Tuberculous Cattle Herds Subjected to Depopulation

Bovine tuberculosis (bTB) is one of the most serious economic animal health problems affecting the cattle industry in Great Britain (GB), with incidence in cattle herds increasing since the mid-1980s. The single intradermal comparative cervical tuberculin (SICCT) test is the primary screening test in the bTB surveillance and control programme in GB and Ireland. The sensitivity (ability to detect infected cattle) of this test is central to the efficacy of the current testing regime, but most previous studies that have estimated test sensitivity (relative to the number of slaughtered cattle with visible lesions [VL] and/or positive culture results) lacked post-mortem data for SICCT test-negative cattle. The slaughter of entire herds (“whole herd slaughters” or “depopulations”) that are infected by bTB are occasionally conducted in GB as a last-resort control measure to resolve intractable bTB herd breakdowns. These provide additional post-mortem data for SICCT test-negative cattle, allowing a rare opportunity to calculate the animal-level sensitivity of the test relative to the total number of SICCT test-positive and negative VL animals identified post-mortem (rSe). In this study, data were analysed from 16 whole herd slaughters (748 SICCT test-positive and 1031 SICCT test-negative cattle) conducted in GB between 1988 and 2010, using a Bayesian hierarchical model. The overall rSe estimate of the SICCT test at the severe interpretation was 85% (95% credible interval [CI]: 78–91%), and at standard interpretation was 81% (95% CI: 70–89%). These estimates are more robust than those previously reported in GB due to inclusion of post-mortem data from SICCT test-negative cattle.
Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the probability of error at certain genomic positions, resulting in false positive variant calls, particularly in mixtures such as samples with RNA editing, tumors, circulating tumor cells, bacteria, mitochondrial heteroplasmy, or pooled DNA. Most algorithms proposed for correction of SSEs require a data set used to calculate association of SSEs with various features in the reads and sequence context. This data set is typically either from a part of the data set being “recalibrated” (Genome Analysis ToolKit, or GATK) or from a separate data set with special characteristics (SysCall). Here, we combine the advantages of these approaches by adding synthetic RNA spike-in standards to human RNA, and use GATK to recalibrate base quality scores with reads mapped to the spike-in standards. Compared to conventional GATK recalibration that uses reads mapped to the genome, spike-ins improve the accuracy of Illumina base quality scores by a mean of 5 Phred-scaled quality score units, and by as much as 13 units at CpG sites. In addition, since the spike-in data used for recalibration are independent of the genome being sequenced, our method allows run-specific recalibration even for the many species without a comprehensive and accurate SNP database. We also use GATK with the spike-in standards to demonstrate that the Illumina RNA sequencing runs overestimate quality scores for AC, CC, GC, GG, and TC dinucleotides, while SOLiD has less dinucleotide SSEs but more SSEs for certain cycles. We conclude that using these DNA and RNA spike-in standards with GATK improves base quality score recalibration.
Collision‐free poisson motion planning in ultra high‐dimensional molecular conformation spaces

The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three‐dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute joints and noncovalent interactions as holonomic constraints, can accurately characterize these native ensembles. However, sampling biomolecules remains challenging owing to their ultra‐high dimensional configuration spaces, and the requirement to avoid (self‐) collisions, which results in low acceptance rates. Here, we present two novel mechanisms to overcome these limitations. First, we introduce temporary constraints between near‐colliding links. The resulting constraint varieties instantaneously redirect the search for collision‐free conformations, and couple motions between distant parts of the linkage. Second, we adapt a randomized Poisson‐disk motion planner, which prevents local oversampling and widens the search, to ultra‐high dimensions. Tests on several model systems show that the sampling acceptance rate can increase from 16% to 70%, and that the conformational coverage in loop modeling measured as average closeness to existing loop conformations doubled. Correlated protein motions identified with our algorithm agree with those from MD simulations. © 2018 Wiley Periodicals, Inc.
Everolimus Inhibits Growth of Gemcitabine‐Resistant Pancreatic Cancer Cells via Induction of Caspase‐Dependent Apoptosis and G2/M Arrest

Pancreatic cancer is the fourth leading cause of cancer‐related death in the United States. While Gemcitabine‐based chemotherapy is the first‐line treatment for locally advanced pancreatic cancer, its resistance is a large obstacle in the field. Understanding the molecular basis of gemcitabine resistance is therefore critical for increasing the efficacy of gemcitabine‐based chemotherapy and improving the survival rate of the cancer patients. Here, we investigated the sensitivity of a pair of established human pancreatic cancer cell lines, MIAPaCa‐E (relatively sensitive to gemcitabine, called GS), and MIAPaCa‐M (highly resistant to gemcitabine, called GR) to various inhibitors of EGFR or PI3K/AKT/mTOR pathways. We found that compared to GS cells, GR cells were resistant to all the tested inhibitors of EGFR, AKT, and PI3K, but were equally, if not more sensitive to the mTOR inhibitor everolimus. Mechanistically, everolimus treatment decreased levels of total mTOR and Ser2248‐phosphorylated mTOR protein in GR over GS cells, suggesting greater inhibition of mTOR by everolimus in GR cells. High levels of Thr389‐ and Thr371‐phosphorylated p70S6 protein (a mTOR substrate) were found in GR cells treated with gemcitabine, but not everolimus, supporting that inhibition of p70S6 protein phosphorylation by everolimus is associated with its ability to overcome gemcitabine resistance. Everolimus also induced higher levels of caspase‐3/‐7 activation in GR over GS cells, and everolimus‐mediated mTOR inhibition lead to G2 arrest in GR cells but G1 arrest in GS cells. Our study suggests the a mTOR inhibitor could improve the efficacy of gemcitabine‐based chemotherapy for otherwise resistant pancreatic cancer. J. Cell. Biochem. 118: 2722–2730, 2017. © 2017 Wiley Periodicals, Inc.
Transforming Growth Factor-f 3 in Human Cutaneous Leishmaniasis

Transforming growthfactor (TGF)-,8 has several downregulatoryfunctions on the immune systenm inhibition ofinterleukin-2 receptor induction, decrease of interferon-yinduced class II antigen expression, inhibition of macrophage activation, as weUl as cytotoxic and lymphokineactivated kilter cell generation. TGF-(8 has also been recognized as an important immunoregulator in murine leishmaniasis, for which it increases susceptibility to disease. In the present study we evaluate the involvement of TGF-j8 in human leishmaniasis in vitro and in patients with cutaneous leishmaniasis. Human macrophages produce active TGF-,3 after infection by Leishmania amazonensis (480 ± 44.7 pg/ml mean ± SEM), L. donovani chagasi (295 + 7.6 pg/ml), or L. braziliensis (196 ± 15.7 pg/ml). When TGF-g3 was added to cultures of human macrophages infected with L. braziliensis it led to an increase of approximately 50% in parasite numbers as compared with untreated cultures. Exogenous TGF1 added to macrophage cultures was able to reverse the effect of interferon-y in controUing Leishmaniagrowth. Even at 100 IU/ml interferon-y the presence ofTGF8 increases the number of intracellular parasites. On the other hand, TNF-a at high concentration (100 IU/ml) totaly blunts the suppressive effect of TGF-4 Immunostaining for TGF-13 was observed in the dermis, produced by fibroblasts and occasionally by inflammatory cells in the biopsies from human leishmaniasis lesions, being present in most of the biopsies taken from patients with early cutaneous leishmaniasis (less than 2 months of ulcer development) and in cases of active mucosal leishmaniasis. Taken together these observations suggest an important rolefor TGF-18 in human leishmaniasis, with its production by infected macrophages being probably related to parasite establishment in the early stages of the disease. (Am J Pathol 1995, 147:947-954)
Comparative study of energy of particles ejected from coulomb explosion of rare gas and metallic clusters irradiated by intense femtosecond laser field

We present our study of high intensity femtosecond laser field interaction with large cluster of Kr and Na (contained 2.103 to 2.107 atoms). When laser intensity is above a critical value, it blows off all of electrons from the cluster and forms a non neutral ion cloud. The irradiation of these clusters by the intense laser field leads to highly excitation energy which can be the source of energetic electrons, electronic emission, highly charge, energetic ions and fragmentation process. During the Coulomb explosion of the resulting highly ionized, high temperature nanoplasma, ions acquire again their energy. It is shown that ultra fast ions are produced. The goal of our study is to investigate in detail a comparative study of the expansion and explosion then the ion energy of metallic and rare gas clusters irradiated by an intense femtosecond laser field. We have found that ions have a kinetic energy up to 105 eV and the Coulomb pressure is little than the hydrodynamic pressure. The Coulomb explosion of a cluster may provide a new high energy ion source.
Living in two worlds: Evolutionary mechanisms act differently in the native and introduced ranges of an invasive plant

Abstract Identifying the factors that influence spatial genetic structure among populations can provide insights into the evolution of invasive plants. In this study, we used the common reed (Phragmites australis), a grass native in Europe and invading North America, to examine the relative importance of geographic, environmental (represented by climate here), and human effects on population genetic structure and its changes during invasion. We collected samples of P. australis from both the invaded North American and native European ranges and used molecular markers to investigate the population genetic structure within and between ranges. We used path analysis to identify the contributions of each of the three factors—geographic, environmental, and human‐related—to the formation of spatial genetic patterns. Genetic differentiation was observed between the introduced and native populations, and their genetic structure in the native and introduced ranges was different. There were strong effects of geography and environment on the genetic structure of populations in the native range, but the human‐related factors manifested through colonization of anthropogenic habitats in the introduced range counteracted the effects of environment. The between‐range genetic differences among populations were mainly explained by the heterogeneous environment between the ranges, with the coefficient 2.6 times higher for the environment than that explained by the geographic distance. Human activities were the primary contributor to the genetic structure of the introduced populations. The significant environmental divergence between ranges and the strong contribution of human activities to the genetic structure in the introduced range suggest that invasive populations of P. australis have evolved to adapt to a different climate and to human‐made habitats in North America.
Care of Preschoolers with Congenital Heart Disease by Kindergarten and Nursery Teachers in Japan

ABSTRACT The purpose of this study was to elucidate the involvement of kindergarten and nursery school teachers with young children with congenital heart disease. The study was designed as a qualitative descriptive study. Interviews of kindergarten and nursery school teachers with experience in the care and education of young children with congenital heart disease were conducted, during which they described their experience. Verbatim transcripts of the interviews were prepared, and the content was categorized. The study participants were 11 kindergarten and nursery school teachers. Extracted from the content of the interviews of the study participants were 282 codes, 33 subcategories, 6 categories, and 2 major categories. In their responses, the teachers indicated that they had been “Providing care for the children while seeking ways to avoid special treatment in a group setting. ” In addition, they established a “Framework for school–parent cooperation in order to promptly accommodate the wishes of parents” of these children. The study showed that the kindergarten and nursery school teachers involved other pupils and monitored the condition of children with congenital heart disease to avoid special treatment of the children in the group setting. In addition, the teachers established a framework for cooperation between the school and parents. In the future, these findings will be used to create a nursing support model for the group life of young children with congenital heart disease.
Alteration in messenger RNA neurotrophin 4 and tyrosine kinase receptors B expression levels following spinal cord injury.

BACKGROUND Neurotrophins as polypeptide growth factors have important roles during nervous system development and are involved in neuronal differentiation and survival and spinal cord reorganization. Neurotrophins have been recognized as factors which are involved in the development of damaged axons and increase the axon growth ability and neuroplasticity. Spinal cord injury (SCI) is associated with numerous physiological damages, leading to neuron death, axon extended destruction healthy and intact neurons demyelination, inflammation, cell death and severe motor/sensory defects. The aim of this study was to investigate the alteration in messenger RNA neurotrophin 4 and tyrosine kinase receptors B expression levels following SCI. METHODS In this research, to know expression level alterations of neurotrophin 4 mRNA and its receptor Trk- B at 6 hours and 1, 3, 7 and 10 days after SCI, we developed competitive RT-qPCR. mRNA was extracted from T9 injury site (epicenter, rostral and caudal to the epicenter) and reversed to cDNA. RESULTS The results showed that the expression of these genes changed after SCI. The NT4 mRNA expression level in the rostral to the epicenter decreased after enhancement in the 1st 6 hours. At the epicenter and in the caudal to the epicenter, it decreased. mRNA expression level of Trk-B decreased after an increase in the initial hours in all the areas. CONCLUSIONS The present results showed that NT4 and Trk-B are expressed temporary and spatially following SCI and the adjustment of these neurotrophins rate in SCI may provide therapeutic benefits.
Real time rectangular document detection on mobile devices

In this paper we propose an algorithm for real-time rectangular document borders detection in mobile device based applications. The proposed algorithm is based on combinatorial assembly of possible quadrangle candidates from a set of line segments and projective document reconstruction using the known focal length. Fast Hough Transform is used for line detection. 1D modification of edge detector is proposed for the algorithm.
Dental Wear: Attrition, Erosion, and Abrasion—A Palaeo-Odontological Approach

This paper reviews the surface ablation of early hominin teeth by attrition, abrasion, and erosive dental wear. The occurrence of these lesions is explored in a sample of South African fossil australopithecine dentitions revealing excessive wear. Interpretation of the nature of the dietary components causing such wear in the absence of carious erosion provides insight into the ecology of the Plio-pleistocene epoch (1–2 million years ago). Fossil teeth inform much of the living past by their retained evidence after death. Tooth wear is the ultimate forensic dental evidence of lives lived.
Lipid Lowering Activity and Free Radical Scavenging Effect of Cinnamomum tamala (Fam: Lauraceae )

Lipid profile is a blood test that measures the amount of lipids, or fats, in your blood. The lipids measured are usually total cholesterol, HDL-C, LDL-C and triglycerides. When levels of these lipids are abnormal, there is an increased risk of heart attack and stroke. In our study, we use methanol crude extract for lipid lowering activity on rabbit and found that lipid profile was reduced by 14.0, 1.0, 4.0 and 15.0 mg/dl for total cholesterol, HDL-C, LDL-C and triglyceride respectively after using the plant extract (dose 500mg/rabbit for 10 days); where atorvastatin (0.005mg/rabbit) was used as standard lipid lowering agent. We also focused on the antioxidant property of crude methanol extract. Here we also carried out free radical-scavenging activity study and found the IC50 value for C. tamala is 6.00 μg/ml where the standard antioxidant (ascorbic acid) gave the value of 3. 21μg/ml. DOI: http://dx.doi. org/10.3329/ijns.v1i4. 9735 IJNS 2011 1(4): 93-96
Decreased left atrial myocardial strain in patients with suboptimal blood pressure control

ABSTRACT Background: Suboptimal blood pressure (BP) control is commonly observed in patients receiving antihypertensive agents, but the relationship between uncontrolled BP and left atrial (LA) impairment remains unknown. Methods: This study enrolled 279 hypertensive patients who had been medicated, as well as 85 matched normal controls. The BP of systolic <140 mmHg and diastolic<90 mmHg was defined as optimal (HT1 group, n=146), otherwise as suboptimal BP control (HT2 group, n = 133). LA myocardial function was assessed by the systolic (SSa), early diastolic (SEa), and late diastolic (SAa) LA strains. Results: Both the HT1 group and HT2 group had higher BP reading, thicker interventricular septum, larger LA volume index, and enhanced active atrial emptying fraction than the control group (all <0.05). When compared with normal subjects, hypertensive patients displayed obvious reduction in the SSa (50.0 ± 10.9 vs. 35.9 ± 8.0%), SEa (30.1 ± 7.7 vs. 18.5 ± 7.1%) and SAa (19.9 ± 6.4 vs. 17.8 ± 4.2%) (all p < 0.001). In addition to a further impaired SEa found in the HT2 group than in the HT1 group (17.2 ± 5.3 vs. 19.8 ± 8.3%, p = 0.002), the treated BP of >140/90 mmHg appeared an independent risk factor associated with the abnormal SEa (odds ratio, 2.957; interval of confidence, 1.614-5.415; p = 0.001). Conclusions: Suboptimal BP control status in hypertensive patients is related to a further reduction of LA myocardial function assessed by the novel 2DSTI free strain, and suboptimal BP might be regarded as a composite risk factor and therefore a simplified treatment target. However, the prognostic value of LA free strain in patients with inability to achieve the BP target needs to be evaluated in future prospective studies.
Prioritized Secondary User Access Control in Cognitive Radio Networks

In cognitive radio networks, a secondary user access control (SUAC) technique has been utilized to improve network management and system security, in which a jamming signal is injected to degrade the spectrum sensing performance of unauthorized secondary users. In the meantime, it ensures reliable spectrum sensing performance for authorized secondary users (A-SUs). In order to introduce spectrum access priorities among A-SUs, a prioritized SUAC (P-SUAC) technique is investigated in this paper. A projection-based jamming cancellation method is considered, where the singular value decomposition operation is applied in computing prioritized projection operators. An orthogonal frequency-division multiplexing technique is considered as a transmission model, and the energy detection method is used for secondary user spectrum sensing. Simulation results illustrate the effectiveness of the proposed P-SUAC method in providing the A-SUs with different access priorities.
Validating new diagnostic imaging criteria for primary progressive aphasia via anatomical likelihood estimation meta‐analyses

Recently, diagnostic clinical and imaging criteria for primary progressive aphasia (PPA) have been revised by an international consortium (Gorno‐Tempini et al. Neurology 2011;76:1006‐14). The aim of this study was to validate the specificity of the new imaging criteria and investigate whether different imaging modalities [magnetic resonance imaging (MRI) and fluorodeoxyglucose positron emission tomography (FDG‐PET)] require different diagnostic subtype‐specific imaging criteria. Anatomical likelihood estimation meta‐analyses were conducted for PPA subtypes across a large cohort of 396 patients: firstly, across MRI studies for each of the three PPA subtypes followed by conjunction and subtraction analyses to investigate the specificity, and, secondly, by comparing results across MRI vs. FDG‐PET studies in semantic dementia and progressive nonfluent aphasia. Semantic dementia showed atrophy in temporal, fusiform, parahippocampal gyri, hippocampus, and amygdala, progressive nonfluent aphasia in left putamen, insula, middle/superior temporal, precentral, and frontal gyri, logopenic progressive aphasia in middle/superior temporal, supramarginal, and dorsal posterior cingulate gyri. Results of the disease‐specific meta‐analyses across MRI studies were disjunct. Similarly, atrophic and hypometabolic brain networks were regionally dissociated in both semantic dementia and progressive nonfluent aphasia. In conclusion, meta‐analyses support the specificity of new diagnostic imaging criteria for PPA and suggest that they should be specified for each imaging modality separately.
The neuroprotective effect of rat adipose tissue-derived mesenchymal stem cell-conditioned medium on cortical neurons using an in vitro model of SCI inflammation

Abstract Objectives In this study, a new approach was used with an in vitro model in which neural cells were exposed to conditioned media from the injured spinal cord (SCI-CM) mimicking a local inflammatory microenvironment . Subsequently, the neuroprotective effect of rat adipose tissue-derived msesenchymal stem cell-conditioned media (ATMSC-CM) was investigated through a cell-free based therapy, which was used to treat cortical neurons and astrocytes under inflammation. Methods Primary cell cultures isolated from postnatal day (P6) Wistar rat brain cortex were exposed to SCI-CM derived from the central lesion, rostral and caudal segments of injured spinal cord. After 48 h incubation, the SCI-CM was replaced and primary cultures were cultivated either in DMEM media alone or in ATMSC-CM for 72 h. The impact of ATMSC-CM on the viability of neurons and astrocytes was assessed using a CyQUANT® Direct Cell Proliferation Assay Kit as well as immunocytochemistry analysis. Results Immunocytochemical analysis revealed significant decrease in the number of MAP2 positive neurons exposed to SCI-CM compared to Control. Protection by ATMSC-CM was associated with increased survival of neurons compared to primary culture cultivated in DMEM media alone. The ATMSC-CM effect on astrocytes was more variable and without any significant impact. Conclusion The results demonstrate that SCI-CM mimicking inflammation can reduce cortical neuron survival, and subsequent exposure to ATMSC-CM can stabilize the neuronal population most likely via released neuroprotective and trophic factors. In addition, astrogliosis was not affected by ATMSC-CM.