Miracle-dz/UniFAR-FTUs huggingface dataset:
Correction for Cohen and Nissim., Towards formalizing the GDPR’s notion of singling out

COMPUTER SCIENCES Correction for “Towards formalizing the GDPR’s notion of singling out,” by Aloni Cohen and Kobbi Nissim, which was first published March 31, 2020; 10.1073/pnas.1914598117 (Proc. Natl. Acad. Sci. U.S.A. 117, 8344–8352). The authors note that, due to a printer’s error, the affiliations for Aloni Cohen and Kobbi Nissim appeared incorrectly. The affiliations for Aloni Cohen should appear as , and the affiliation for Kobbi Nissim should appear as . The corrected author and affiliation lines appear below. The online version has been corrected.
Vascular Lipidomic Profiling of Potential Endogenous Fatty Acid PPAR Ligands Reveals the Coronary Artery as Major Producer of CYP450-Derived Epoxy Fatty Acids

A number of oxylipins have been described as endogenous PPAR ligands. The very short biological half-lives of oxylipins suggest roles as autocrine or paracrine signaling molecules. While coronary arterial atherosclerosis is the root of myocardial infarction, aortic atherosclerotic plaque formation is a common readout of in vivo atherosclerosis studies in mice. Improved understanding of the compartmentalized sources of oxylipin PPAR ligands will increase our knowledge of the roles of PPAR signaling in diverse vascular tissues. Here, we performed a targeted lipidomic analysis of ex vivo-generated oxylipins from porcine aorta, coronary artery, pulmonary artery and perivascular adipose. Cyclooxygenase (COX)-derived prostanoids were the most abundant detectable oxylipin from all tissues. By contrast, the coronary artery produced significantly higher levels of oxylipins from CYP450 pathways than other tissues. The TLR4 ligand LPS induced prostanoid formation in all vascular tissue tested. The 11-HETE, 15-HETE, and 9-HODE were also induced by LPS from the aorta and pulmonary artery but not coronary artery. Epoxy fatty acid (EpFA) formation was largely unaffected by LPS. The pig CYP2J homologue CYP2J34 was expressed in porcine vascular tissue and primary coronary artery smooth muscle cells (pCASMCs) in culture. Treatment of pCASMCs with LPS induced a robust profile of pro-inflammatory target genes: TNFα, ICAM-1, VCAM-1, MCP-1 and CD40L. The soluble epoxide hydrolase inhibitor TPPU, which prevents the breakdown of endogenous CYP-derived EpFAs, significantly suppressed LPS-induced inflammatory target genes. In conclusion, PPAR-activating oxylipins are produced and regulated in a vascular site-specific manner. The CYP450 pathway is highly active in the coronary artery and capable of providing anti-inflammatory oxylipins that prevent processes of inflammatory vascular disease progression.
Redescription of Rhipidocotyle galeata (Rudolphi, 1819) (Digenea, Bucephalidae), the type species of Rhipidocotyle Diesing, 1907

Derbel H. , Châari M. & Neifar L. 2011. — Redescription of Rhipidocotyle galeata (Rudolphi, 1819) (Digenea, Bucephalidae), the type species of Rhipidocotyle Diesing, 1907. Zoosystema 33 (2): 133–139. ABSTRACT Rhipidocotyle galeata (Rudolphi, 1819), the type species of the genus, is redescribed using material from Lichia amia (Linnaeus, 1758) (Actinopterygii, Perciformes) collected from the Gulf of Gabès in the Mediterranean Sea off Tunisia. Rhipidocotyle galeata is compared with other nominal species of the genus, including R. genovi, R. minima, R. triglae and R. viperae. This redescription provides additional information about the position and the distribution of the vitelline follicles, which form an arc that does not extend anteriorly past the level of the ovary, an uterus that extends almost to the posterior margin of the rhynchus and an ovary that is positioned adjacent to the anterior testis. A key to the eight Rhipidocotyle species from the Mediterranean Sea is presented.
MaRe: Processing Big Data with application containers on Apache Spark

Abstract Background Life science is increasingly driven by Big Data analytics, and the MapReduce programming model has been proven successful for data-intensive analyses. However, current MapReduce frameworks offer poor support for reusing existing processing tools in bioinformatics pipelines. Furthermore, these frameworks do not have native support for application containers, which are becoming popular in scientific data processing. Results Here we present MaRe, an open source programming library that introduces support for Docker containers in Apache Spark. Apache Spark and Docker are the MapReduce framework and container engine that have collected the largest open source community; thus, MaRe provides interoperability with the cutting-edge software ecosystem. We demonstrate MaRe on 2 data-intensive applications in life science, showing ease of use and scalability. Conclusions MaRe enables scalable data-intensive processing in life science with Apache Spark and application containers. When compared with current best practices, which involve the use of workflow systems, MaRe has the advantage of providing data locality, ingestion from heterogeneous storage systems, and interactive processing. MaRe is generally applicable and available as open source software.
Breed- and trait-specific associations define the genetic architecture of calving performance traits in cattle

Abstract Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P < 5 × 10−8) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P > × 10−6) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P < 5 × 10−8). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.
Motor Competence, Physical Activity, and Fitness across Early Childhood

ABSTRACT Objectives To examine if the associations between motor competence and physical activity and musculoskeletal fitness change over time, whether motor competence is associated with longitudinal trajectories of physical activity and fitness, and mediating pathways among these constructs across early childhood. Methods Four hundred and eighteen children 3 to 5 yr of age (210 boys; age, 4.5 ± 1.0 yr) were recruited and completed three annual assessments as part of the Health Outcomes and Physical activity in Preschoolers study. Motor competence was assessed using the Bruininks–Oseretsky Test of Motor Proficiency Second Edition—Short Form. Musculoskeletal fitness (short-term muscle power) was evaluated using a modified 10-s Wingate protocol on a cycle ergometer. Physical activity was measured over 7 d using accelerometers. Results At baseline, the cross-sectional relationship between motor competence and vigorous physical activity was not significant; however, a significant, weak positive association emerged across time. Results from longitudinal mixed-effect models found motor competence to be a significant positive predictor of musculoskeletal fitness and vigorous physical activity and to be associated with steeper increases in physical activity across time. Motor competence was independently associated with musculoskeletal fitness and physical activity during this early childhood period. Conclusions Motor competence is an important independent predictor of physical activity and musculoskeletal fitness levels across early childhood. Motor competence may be an important target for early interventions to improve both physical activity and fitness in the early years.
High Frequency β-glucuronidase Reporter Gene Expression in Shoot Tip, Leaf, and Hypocotyl Explants of Jatropha curcas L.

Development of a suitable genetic transformation system is the backbone of transgenic technology for efficient recovery of Jatropha curcas plants with desirable traits. Although in vitro plant regeneration protocols for shoot tip, leaf, and hypocotyl explants of J. curcas have been reported, these protocol have not been translated into efficient genetic transformation systems. The objective of this study was to standardize the parameters influencing transient β-glucuronidase reporter gene expression following Agrobacterium-mediated genetic transformation using shoot tip, leaf, and hypocotyl explants of Jatropha curcas. Disarmed Agrobacterium tumefaciens strain EHA105, harboring pCAMBIA2301 carrying neomycin phosphotransferase (nptII) as a selectable marker and the β-glucuronidase (GUS) as a reporter gene, were used for transformation. Frequencies of GUS gene expression of 86.7%, 78.3%, and 74.2% were obtained for leaf, hypocotyls, and shoot tip explants, respectively. The transgenic nature of the kanamycin-resistant explants was also confirmed by using polymerase chain reaction (PCR) assay. Because, to date, there is no report on Agrobacterium-mediated transformation of shoot tip, leaf, and hypocotyl explants of Jatropha curcas, our findings/protocol should be useful for recovering stable transgenic Jatropha curcas plants from these explants.
Characterization of the TCR β Chain CDR3 Repertoire in Subarachnoid Hemorrhage Patients with Delayed Cerebral Ischemia

Little is known of the adaptive immune response to subarachnoid hemorrhage (SAH). This study was the first to investigate whether T cell receptor (TCR) immune repertoire may provide a better understanding of T cell immunology in delayed cerebral ischemia (DCI). We serially collected peripheral blood in five SAH patients with DCI. High-throughput sequencing was used to analyze the TCR β chain (TCRB) complimentary determining regions (CDR) 3 repertoire. We evaluated the compositions and variations of the repertoire between admission and the DCI period, for severe DCI and non-severe DCI patients. Clonality did not differ significantly between admission and DCI. Severe DCI patients had significantly lower clonality than non-severe DCI patients (p value = 0.019). A read frequency of 0.005% ≤ – < 0.05% dominated the clonal expansion in non-severe DCI patients. Regarding repertoire diversity, severe DCI had a higher diversity score on admission than non-severe DCI. The CDR3 lengths were similar between admission and DCI. Among 728 annotated V-J gene pairs, we found that the relative frequencies of two V-J pairs were different at the occurrence of DCI than at admission, with T cells increasing by over 15%. TCRB CDR3 repertoires may serve as biomarkers to identify severe DCI patients.
SARS Unique Domain (SUD) of Severe Acute Respiratory Syndrome Coronavirus Induces NLRP3 Inflammasome-Dependent CXCL10-Mediated Pulmonary Inflammation

Severe acute respiratory syndrome–associated coronavirus (SARS-CoV) initiates the cytokine/chemokine storm-mediated lung injury. The SARS-CoV unique domain (SUD) with three macrodomains (N, M, and C), showing the G-quadruplex binding activity, was examined the possible role in SARS pathogenesis in this study. The chemokine profile analysis indicated that SARS-CoV SUD significantly up-regulated the expression of CXCL10, CCL5 and interleukin (IL)-1β in human lung epithelial cells and in the lung tissues of the mice intratracheally instilled with the recombinant plasmids. Among the SUD subdomains, SUD-MC substantially activated AP-1-mediated CXCL10 expression in vitro. In the wild type mice, SARS-CoV SUD-MC triggered the pulmonary infiltration of macrophages and monocytes, inducing CXCL10-mediated inflammatory responses and severe diffuse alveolar damage symptoms. Moreover, SUD-MC actuated NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome-dependent pulmonary inflammation, as confirmed by the NLRP3 inflammasome inhibitor and the NLRP3−/− mouse model. This study demonstrated that SARS-CoV SUD modulated NLRP3 inflammasome-dependent CXCL10-mediated pulmonary inflammation, providing the potential therapeutic targets for developing the antiviral agents.
Engineered human FcγRIIa fusion: A novel strategy to extend serum half‐life of therapeutic proteins

The immunoglobulin G (IgG) molecule has a long circulating serum half‐life (~3 weeks) through pH‐ dependent FcRn binding‐mediated recycling. To hijack the intracellular trafficking and recycling mechanism of IgG as a way to extend serum persistence of non‐antibody therapeutic proteins, we have evolved the ectodomain of a low‐affinity human FcγRIIa for enhanced binding to the lower hinge and upper CH2 region of IgG, which is very far from the FcRn binding site (CH2–CH3 interface). High‐throughput library screening enabled isolation of an FcγRIIa variant (2A45.1) with 32‐fold increased binding affinity to human IgG1 Fc (equilibrium dissociation constant: 9.04 × 10−7 M for wild type FcγRIIa and 2.82 × 10−8 M for 2A45.1) and significantly improved affinity to mouse serum IgG compared to wild type human FcγRIIa. The in vivo pharmacokinetic profile of PD‐L1 fused with engineered FcγRIIa (PD‐L1–2A45.1) was compared with that of PD‐L1 fused with wild type FcγRIIa (PD‐L1–wild type FcγRIIa) and human PD‐L1 in mice. PD‐L1–2A45.1 showed 11.7‐ and 9.7‐fold prolonged circulating half‐life (t1/2) compared to PD‐L1 when administered intravenously and intraperitoneally, respectively. In addition, the AUCinf of PD‐L1–2A45.1 was two‐fold higher compared to that of PD‐L1–wild type FcγRIIa. These results demonstrate that engineered FcγRIIa fusion offers a novel and successful strategy for prolonging serum half‐life of therapeutic proteins.
Comparative Effects of Feeding Diets Containing Flavomycin, Bioteksin-L and Dry Yeast (Saccharomyces cerevisiae) on Broiler Performance

Abstract Denli, M. , Çelik, K. and Okan, F. 2003. Comparative effects of feeding diets containing flavomycin, bioteksin-L and dry yeast (Saccharomyces cerevisiae) on broiler performance. J. Appl. Anim. Res., 23: 139–144. A 6-week study was conducted to determine the effects of feeding diets containing commercial probiotic (Bioteksin-L, 2xlO8cfu/g), antibiotic (Flavomycin) and dry yeast (Saccharomyces cerevisiae) performance, abdominal fat weight, carcass weight and carcass yield of broiler chicks. Four dietary treatments control, containing 0.15% commercial probiotic (bioteksin-L), 0.15% antibiotic (Flavomycin) or 0.3% dry yeast were randomly assigned to four groups of chicks. A significant increase in body weight gain, feed conversion rate and carcass weight of birds was observed in birds fed flavomycin and dry yeast at the end of S-wk period (P<0.05). Biyoteksin-L and Saccharomyces cerevisiae supplementation to diets tended to decrease, abdominal fat weight and abdominal fat percentage (P<0.5).
Evaluation of Three Different Structures Used for Walleye Age Estimation with Emphasis on Removal and Processing Times

Abstract We compared the removal and processing times required when scales, sagittal otoliths, and dorsal spines were used as age estimation structures for 160 walleyes Stizostedion vitreum collected from six water bodies in South Dakota. Removal and processing times were calculated by 10 fish groups. Dorsal spines required the least amount of time for removal, followed by scales and otoliths. Whole-view otoliths required no further manipulation prior to estimating age, while the sectioning of dorsal spines and scale pressing required 12.5 and 16.6 min of additional processing time, respectively. Dorsal spines and scales also required significantly more time to read than otoliths. In terms of total processing time, whole-view otoliths proved the most time-efficient approach for estimating the age of walleyes. Scales were slightly more time-efficient than dorsal-spine sections, and sectioning otoliths would add additional processing time. Sectioning may not have been necessary in this evaluation because ag.
Microbial Metabolic Potential of Phenol Degradation in Wastewater Treatment Plant of Crude Oil Refinery: Analysis of Metagenomes and Characterization of Isolates

The drilling, processing and transportation of oil are the main sources of pollution in water and soil. The current work analyzes the microbial diversity and aromatic compounds degradation potential in the metagenomes of communities in the wastewater treatment plant (WWTP) of a crude oil refinery. By focusing on the degradation of phenol, we observed the involvement of diverse indigenous microbial communities at different steps of the WWTP. The anaerobic bacterial and archaeal genera were replaced by aerobic and facultative anaerobic bacteria through the biological treatment processes. The phyla Proteobacteria, Bacteroidetes and Planctomycetes were dominating at different stages of the treatment. Most of the established protein sequences of the phenol degradation key enzymes belonged to bacteria from the class Alphaproteobacteria. From 35 isolated strains, 14 were able to grow on aromatic compounds, whereas several phenolic compound-degrading strains also degraded aliphatic hydrocarbons. Two strains, Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13, were able to degrade various aromatic and aliphatic pollutants and were further characterized by whole genome sequencing and cultivation experiments in the presence of phenol to ascertain their metabolic capacity in phenol degradation. When grown alone, the intermediates of catechol degradation, the meta or ortho pathways, accumulated into the growth environment of these strains. In the mixed cultures of the strains ICP1 and ICTN13, phenol was degraded via cooperation, in which the strain ICP1 was responsible for the adherence of cells and ICTN13 diminished the accumulation of toxic intermediates.
Cabot's Tragopan

Cabot’s Tragopan (Tragopan caboti) (Galliformes: Phasianidae) is one of the endemic pheasant species in China. It is categorized as Vulnerable in the IUCN Red list (IUCN, 2008) and is also listed in Appendix I of CITES (Fuller and Garson, 2000). It is a national first grade protected species in China. Its population size is less than 4000 and this pheasant is only found in several small patches in southeastern China (Zheng and Wang, 1998; Fig. 1). The typical habitat of Cabot’s Tragopan is a broadleaf evergreen and mixed broadleaf coniferous forest at elevations between 800–2000 m (Zhang and Zheng, 2007). Much of its preferred habitat has been destroyed through conversion to agricultural land or for the construction of houses, roads and railways. It is mostly found in forests dominated by Fagaceae, Lauraceae, Theaceae, Aquifoliaceae, Symplocaceae, Rosaceae and Ericaceae families. Habitat use is similar throughout the year and individuals do not move to lower areas during the winter, in contrast with other tragopan species. During the late autumn and winter, habitat use is correlated significantly with the presence of Daphniphyllum macropodum, a tree whose fruits and leaves are an important food for the pheasant during this difficult time. In January 2008, southern China experienced a huge cold snap. Cabot’s Tragopan is the most frequently occurring species in the research area (from 700–2000 m), but was not affected by this disaster as were other pheasants, such as the Silver Pheasant and the Chinese Bamboo Partridge, which are found in lower areas. The home range size varied from 0.029 to 0.39 km, with a mean of 0.24 km. The home range of neighboring males always overlaps to some degree (Sun and Zheng, 1992). The furthest distance recorded of an individual moving was less than 3 km. Recent research shows that Cabot’s Tragopan cannot adapt well to habitat fragmentation since it hardly passes the mid-level ecological barrier. Because of its weak dispersal capability, habitat fragmentation is the most important factor affecting this pheasant. In recent decades, much of its typical habitat has been destroyed, converted to agricultural use, bamboo forest or separated by anthropogenic activities such as road and railway construction. As a result, the pheasant has been absent from some regions where individuals have been detected in earlier years (Qian and Zheng, 1993). Cabot’s Tragopan built nests in large trees (Fig. 2b), between 2.4 m and 10 m above the ground (mean 4.4±2.1 m), found near ridge tops. Height and diameters at breast height of a tree, nest height, canFig. 1 Distribution areas of Cabot’s Tragopan
Risk Factors for Duty-Related Posttraumatic Stress Disorder among Police Officers in the Mt. Ontake Eruption Disaster-Support Task Force

Mount Ontake in Nagano Prefecture, Japan erupted on 27 September 2014. Many police officers were called in for duty as a disaster-support task force. We investigated the association between the peritraumatic situation and posttraumatic stress disorder (PTSD) symptoms in these police officers. In January 2015, a health survey (OHS) on disaster stress related to the Mt. Ontake eruption disaster support work was distributed to all of the police officers and staff involved in the disaster support. We analyzed the 213 participants who had PTSD symptoms following the eruption and no missing OHS data. Logistic regression analyses were conducted to clarify the relationship between the participants’ symptom severity and their peritraumatic situation (i.e., stressors and daily support prior to the eruption, disaster-support work duties, and postdisaster stress relief). The symptom severity was associated with ‘more than seven cumulative days at work’ (odds ratio [OR] = 2.47, 1.21–5.06), ‘selecting drinking and/or smoking as stress relief after disaster-support work’ (OR = 2.35, 1.09–5.04), and ‘female’ (OR = 3.58, 1.19–10.77). As disaster-support work, ‘supporting the victims’ families’ (OR = 1.99, 0.95–4.21) tended to be associated with symptom severity. The number of days of disaster-support work, stress-relief behavior, and gender were associated with the severity of PTSD symptoms.