Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification, characterization, and expression of sarcomeric tropomyosin isoforms in zebrafish

Tropomyosin is a component of thin filaments that constitute myofibrils, the contractile apparatus of striated muscles. In vertebrates, except for fish, four TPM genes TPM1, TPM2, TPM3, and TPM4 are known. In zebrafish, there are six TPM genes that include the paralogs of the TPM1 (TPM1‐1 and TPM1‐2), the paralogs of the TPM4 gene (TPM4‐1 and TPM4‐2), and the two single copy genes TPM2 and TPM3. In this study, we have identified, cloned, and sequenced the TPM1‐1κ isoform of the TPM1‐1 gene and also discovered a new isoform TPM1‐2ν of the TPM1‐2. Further, we have cloned and sequenced the sarcomeric isoform of the TPM4‐2 gene designated as TPM4‐2α. Using conventional RT‐PCR, we have shown the expression of the sarcomeric isoforms of TPM1‐1, TPM1‐2, TPM2, TPM3, TPM4‐1, and TPM4‐2 in heart and skeletal muscles. By qRT‐PCR using both relative expression as well as the absolute copy number, we have shown that TPM1‐1α, TPM1‐2α, and TPM1‐2ν are expressed mostly in skeletal muscle; the level of expression of TPM1‐1κ is significantly lower compared to TPM1‐1α in skeletal muscle. In addition, both TPM4‐1α and TPM4‐2α are predominantly expressed in heart. 2D Western blot analyses using anti‐TPM antibody followed by Mass Spectrometry of the proteins from the antibody‐stained spots show that TPM1‐1α and TPM3α are expressed in skeletal muscle whereas TPM4‐1α and TPM3α are expressed in zebrafish heart. To the best of our knowledge, this is by far the most comprehensive analysis of tropomyosin expression in zebrafish, one of the most popular animal models for gene expression study.
Changes in Postharvest Qualities of Stored Fresh Maize (Zea Mays L.) at Tropical Ambient Condition

The effect of passive modified atmosphere packaging on some postharvest qualities of stored fresh maize was investigated at tropical ambient temperature (28±2 °C) and 80% RH. Changes in the appearances of husk, silk and kernel, kernel firmness, weight and microbial growth were monitored. Freshly harvested yellow maize (FHYM) served as control. Results showed that packaging film greatly affected the appearances of the husk, silk, kernel and kernel firmness compare to the control sample. The highest weight loss was observed in dehusked maize while the maize samples in packaging film had the least weight loss. Lactobacillus sp. , Micrococcus liteus, Streptococcus sp. , Serratia marcescens, Bacillus sp. and Saccharomyces cerevisiae were the bacteria isolated from the stored fresh maize while the suspected fungal include Rhizopus stolonifer, Penicillium notatum and Fusarium sp. Higher bacteria counts were observed in samples packaged with 25 and 30 μm LDPE while the least was found in unpackaged undehusked maize. The current packaging conditions had no impact on the shelf life of fresh maize.
A Security Credential Management System for V2X Communications

The U.S. Department of Transportation (USDOT) issued a proposed rule on January 12, 2017 to mandate vehicle-to-vehicle safety communications in light vehicles in the U.S. Cybersecurity and privacy are major challenges for such a deployment. We present a Security Credential Management System (SCMS) for vehicle-to-everything (V2X) communications in this paper, which has been developed by the Crash Avoidance Metrics Partners LLC under a cooperative agreement with the USDOT. This system design is currently transitioning from research to proof-of-concept and is a leading candidate to support the establishment of a nationwide Public Key Infrastructure for V2X security. It issues digital certificates to participating vehicles and infrastructure devices for trustworthy communications among them, which is necessary for safety and mobility applications that are based on V2X communications. The SCMS supports four main use cases, namely, bootstrapping, certificate provisioning, misbehavior reporting, and revocation. The main design goal is to provide both security and privacy to the largest extent reasonable and possible. To achieve a reasonable level of privacy in this context, vehicles are issued pseudonym certificates, and the generation and provisioning of those certificates are divided among multiple organizations. Given the large number of pseudonym certificates per vehicle, one of the main challenges is to facilitate efficient revocation of misbehaving or malfunctioning vehicles, while preserving privacy against attacks from insiders. The proposed SCMS supports all identified V2X use-cases and certificate types necessary for V2X communication security. This paper is based upon work supported by the USDOT. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors (“we”) and do not necessarily reflect the view of the USDOT.
Archaeological and anthropological studies on the Harappan cemetery of Rakhigarhi, India

An insufficient number of archaeological surveys has been carried out to date on Harappan Civilization cemeteries. One case in point is the necropolis at Rakhigarhi site (Haryana, India), one of the largest cities of the Harappan Civilization, where most burials within the cemetery remained uninvestigated. Over the course of the past three seasons (2013 to 2016), we therefore conducted excavations in an attempt to remedy this data shortfall. In brief, we found different kinds of graves co-existing within the Rakhigarhi cemetery in varying proportions. Primary interment was most common, followed by the use of secondary, symbolic, and unused (empty) graves. Within the first category, the atypical burials appear to have been elaborately prepared. Prone-positioned internments also attracted our attention. Since those individuals are not likely to have been social deviants, it is necessary to reconsider our pre-conceptions about such prone-position burials in archaeology, at least in the context of the Harappan Civilization. The data presented in this report, albeit insufficient to provide a complete understanding of Harappan Civilization cemeteries, nevertheless does present new and significant information on the mortuary practices and anthropological features at that time. Indeed, the range of different kinds of burials at the Rakhigarhi cemetery do appear indicative of the differences in mortuary rituals seen within Harappan societies, therefore providing a vivid glimpse of how these people respected their dead.
Digestible lysine requirement of male and female broiler chicks during the period three to six weeks posthatching.

Experiments were conducted to determine the dietary digestible lysine requirement of male and female broilers (Ross x Ross) during the period 22 to 43 d posthatching. An amino acid-fortified basal diet containing corn, feather meal, and soybean meal as intact protein sources provided . 63% total lysine, 20% CP, and 3,200 kcal MEn/kg. The basal diet contained . 51% true digestible lysine as determined with a precision-fed cecectomized adult cockerel assay. Growth rate and feed efficiency of birds fed the basal diet fortified with a surfeit level of L-lysine were equal to those of birds fed a methionine-supplemented corn-soybean meal positive control diet (20% CP; 3,200 kcal MEn/kg). Graded levels of synthetic L-lysine (0, .1, .2, .3, .4, .5, .6%) were added to the basal diet to produce growth response curves. Subjecting the growth data to broken-line analysis indicated that the digestible lysine requirement for maximum body weight gain was . 85% for males and . 78% for females. The requirement for optimum feed efficiency was higher: . 89% for males and . 85% for female broilers. Breast meat (Pectoralis major) yield increased quadratically in response to lysine addition, and the responses suggested that the lysine requirement for maximal breast yield was not greatly different from that predicted from the feed efficiency data. Abdominal fat (percentage of live body weight) increased from the first to the second increment of lysine, but it then declined as lysine level was increased further.
On the Feasibility of Generic Deep Disaggregation for Single-Load Extraction

Recently, and with the growing development of big energy datasets, data-driven learning techniques began to represent a potential solution to the energy disaggregation problem outperforming engineered and hand-crafted models. However, most proposed deep disaggregation models are load-dependent in the sense that either expert knowledge or a hyper-parameter optimization stage is required prior to training and deployment (normally for each load category) even upon acquisition and cleansing of aggregate and sub-metered data. In this paper, we present a feasibility study on the development of a generic disaggregation model based on data-driven learning. Specifically, we present a generic deep disaggregation model capable of achieving state-of-art performance in load monitoring for a variety of load categories. The developed model is evaluated on the publicly available UK-DALE dataset with a moderately low sampling frequency and various domestic loads.
Progress and prospects for the discovery of biomarkers for gastric cancer: a focus on proteomics

ABSTRACT Introduction: Patient outcomes from gastric cancer vary due to the complexity of stomach carcinogenesis. Recent research using proteomic technologies has targeted components of all of these systems in order to develop biomarkers to aid the early diagnosis of gastric cancer and to assist in prognostic stratification. Areas covered: This review is comprised of evidence obtained from literature searches from PubMed. It covers the evidence of diagnostic, prognostic, and predictive biomarkers for gastric cancer using proteomic technologies, and provides up-to-date references. Expert commentary: The proteomic technologies have not only enabled the screening of a large number of samples, but also enabled the identification of diagnostic, prognostic and predictive biomarkers for gastric cancer. While major challenges still remain, to date, proteomic studies in gastric cancer have provided a wealth of information in revealing proteome alterations associated with the disease.
The status of tularemia in Europe in a one-health context: a review

SUMMARY The bacterium Francisella tularensis causes the vector-borne zoonotic disease tularemia, and may infect a wide range of hosts including invertebrates, mammals and birds. Transmission to humans occurs through contact with infected animals or contaminated environments, or through arthropod vectors. Tularemia has a broad geographical distribution, and there is evidence which suggests local emergence or re-emergence of this disease in Europe. This review was developed to provide an update on the geographical distribution of F. tularensis in humans, wildlife, domestic animals and vector species, to identify potential public health hazards, and to characterize the epidemiology of tularemia in Europe. Information was collated on cases in humans, domestic animals and wildlife, and on reports of detection of the bacterium in arthropod vectors, from 38 European countries for the period 1992–2012. Multiple international databases on human and animal health were consulted, as well as published reports in the literature. Tularemia is a disease of complex epidemiology that is challenging to understand and therefore to control. Many aspects of this disease remain poorly understood. Better understanding is needed of the epidemiological role of animal hosts, potential vectors, mechanisms of maintenance in the different ecosystems, and routes of transmission of the disease.
Chick PTPς Regulates the Targeting of Retinal Axons within the Optic Tectum

Chick PTPς (cPTPς), also known as CRYPα, is a receptor-like protein tyrosine phosphatase found on axons and growth cones. Putative ligands for cPTPς are distributed within basement membranes and on glial end feet of the retina, optic nerve, and optic tectum, suggesting that cPTPς signaling is occurring along the whole retinotectal pathway. We have shown previously that cPTPς plays a role in supporting the retinal phase of axon outgrowth. Here we have now addressed the role of cPTPς within retinal axons as they undergo growth and topographic targeting in the optic tectum. With the use of retroviruses, a secretable cPTPς ectodomain was ectopically expressedin ovo in the developing chick optic tectum, with the aim of directly disrupting the function of endogenous cPTPς. In ovo, the secreted ectodomains accumulated at tectal sites in which cPTPς ligands are also specifically found, suggesting that they are binding to these endogenous ligands. Anterograde labeling of retinal axons entering these optic tecta revealed abnormal axonal phenotypes. These included the premature stalling and arborization of fibers, excessive pretectal arbor formation, and diffuse termination zones. Most of the defects were rostral of the predicted termination zone, indicating that cPTPς function is necessary for sustaining the growth of retinal axons over the optic tectum and for directing axons to their correct sites of termination. This demonstrates that regulation of cPTPς signaling in retinal axons is required for their topographic mapping, the first evidence of this function for a receptor-like protein tyrosine phosphatase in the retinotectal projection.
Distinguishing Question Subjectivity from Difficulty for Improved Crowdsourcing

The questions in a crowdsourcing task typically exhibit varying degrees of difficulty and subjectivity. Their joint effects give rise to the variation in responses to the same question by different crowd-workers. This variation is low when the question is easy to answer and objective, and high when it is difficult and subjective. Unfortunately, current quality control methods for crowdsourcing consider only the question difficulty to account for the variation. As a result,these methods cannot distinguish workers personal preferences for different correct answers of a partially subjective question from their ability/expertise to avoid objectively wrong answers for that question. To address this issue, we present a probabilistic model which (i) explicitly encodes question difficulty as a model parameter and (ii) implicitly encodes question subjectivity via latent preference factors for crowd-workers. We show that question subjectivity induces grouping of crowd-workers, revealed through clustering of their latent preferences. Moreover, we develop a quantitative measure of the subjectivity of a question. Experiments show that our model(1) improves the performance of both quality control for crowd-sourced answers and next answer prediction for crowd-workers,and (2) can potentially provide coherent rankings of questions in terms of their difficulty and subjectivity, so that task providers can refine their designs of the crowdsourcing tasks, e.g. by removing highly subjective questions or inappropriately difficult questions.
Monobloc Frontofacial or Le Fort III Distraction Osteogenesis in Syndromic Craniosynostosis: Three-Dimensional Evaluation of Treatment Outcome and the Need for Central Distraction

Background: The objectives of this study were to investigate the treatment effect, morphology, and volumetric outcomes of monobloc frontofacial or Le Fort III distraction osteogenesis in syndromic craniosynostosis by 3-dimensional evaluation. Materials and Methods: Nine consecutive patients underwent monobloc frontofacial or Le Fort III distraction during 2003 to 2012 were included and evaluated. The patient's evaluation is a minimum of a 4-year follow-up. Pretreatment, post-treatment advancement, and relapse were quantified. The changes in intracranial volume, upper airway volume, globe protrusion, advancement at bilateral malar eminence, and central face were calculated from computerized tomography before and after treatment. Results: After distraction, the intracranial volume was increased by 16.4% in average, and the upper airway volume increased by 64.1%. Orbital protrusion improved by 9.9 mm in the left eye and 10.5 mm in the right eye in comparison to the preoperative status. Bilateral malar eminences advancement was greater than the dorsum advancement by 7.1 mm. Conclusion: The external distraction osteogenesis device caused significant technical difficulties with advancement of the midface in growing bones. The central midface did not advance as hoped for. This finding may suggest a need for modification in the distraction device in order to improve the central facial distraction vector.
Non-degradative Ubiquitination of Protein Kinases

Growing evidence supports other regulatory roles for protein ubiquitination in addition to serving as a tag for proteasomal degradation. In contrast to other common post-translational modifications, such as phosphorylation, little is known about how non-degradative ubiquitination modulates protein structure, dynamics, and function. Due to the wealth of knowledge concerning protein kinase structure and regulation, we examined kinase ubiquitination using ubiquitin remnant immunoaffinity enrichment and quantitative mass spectrometry to identify ubiquitinated kinases and the sites of ubiquitination in Jurkat and HEK293 cells. We find that, unlike phosphorylation, ubiquitination most commonly occurs in structured domains, and on the kinase domain, ubiquitination is concentrated in regions known to be important for regulating activity. We hypothesized that ubiquitination, like other post-translational modifications, may alter the conformational equilibrium of the modified protein. We chose one human kinase, ZAP-70, to simulate using molecular dynamics with and without a monoubiquitin modification. In Jurkat cells, ZAP-70 is ubiquitinated at several sites that are not sensitive to proteasome inhibition and thus may have other regulatory roles. Our simulations show that ubiquitination influences the conformational ensemble of ZAP-70 in a site-dependent manner. When monoubiquitinated at K377, near the C-helix, the active conformation of the ZAP-70 C-helix is disrupted. In contrast, when monoubiquitinated at K476, near the kinase hinge region, an active-like ZAP-70 C-helix conformation is stabilized. These results lead to testable hypotheses that ubiquitination directly modulates kinase activity, and that ubiquitination is likely to alter structure, dynamics, and function in other protein classes as well.
Extended low-resolution structure of a Leptospira antigen offers high bactericidal antibody accessibility amenable to vaccine design

Pathogens rely on proteins embedded on their surface to perform tasks essential for host infection. These obligatory structures exposed to the host immune system provide important targets for rational vaccine design. Here, we use a systematically designed series of multi-domain constructs in combination with small angle X-ray scattering (SAXS) to determine the structure of the main immunoreactive region from a major antigen from Leptospira interrogans, LigB. An anti-LigB monoclonal antibody library exhibits cell binding and bactericidal activity with extensive domain coverage complementing the elongated architecture observed in the SAXS structure. Combining antigenic motifs in a single-domain chimeric immunoglobulin-like fold generated a vaccine that greatly enhances leptospiral protection over vaccination with single parent domains. Our study demonstrates how understanding an antigen’s structure and antibody accessible surfaces can guide the design and engineering of improved recombinant antigen-based vaccines.
Vitamin B12. The absorption of 57Co or 60Co-B12 by thlaying hen and mature rooster.

Abstract YACOWITZ et al. (1952) demonstrated that eggs from the same hen showed remarkable individuality with respect to their content of vitamin B12. Eggs from individual hens depleted of vitamin B12 for one month contained from 0.77 to 4.06 millimicrograms of B12 per gram of egg yolk. Evans et al. (1955) also noted that individual hens differed in the ability to place vitamin B12 in their eggs. They also raised the question as to whether this reflected a difference in digestion, absorption, or metabolism of vitamin B12 by individual hens. The studies reported in this paper were conducted to gain information on the absorption and retention of 57 Co-B12 and 60 Co-B12 by laying hens and mature roosters and to determine the amounts of these tagged vitamins placed in eggs by laying hens. EXPERIMENTAL Twelve mature Single Comb White Leghorn chickens of each sex were utilized for this study. The animals were housed…
Association Between Malignancy and Topical Use of Pimecrolimus.

IMPORTANCE A black box warning describes a potential risk of malignancy associated with topical use of pimecrolimus to treat atopic dermatitis due to its similarity to oral calcineurin inhibitors used in solid-organ transplantation and spontaneous reporting of malignancies, including lymphomas and cutaneous malignancies. OBJECTIVE To evaluate the risk of malignancy in a postmarketing study of children exposed to pimecrolimus. DESIGN, SETTING, AND PARTICIPANTS A longitudinal cohort study among a nationwide ongoing long-term cohort of children enrolled in the Pediatric Eczema Elective Registry (PEER) who had a history of atopic dermatitis and pimecrolimus use with data available up through May 2014. MAIN OUTCOMES AND MEASURES Reports of malignancy among those in the PEER compared with expected rates from the Surveillance, Epidemiology, and End Results (SEER) program. RESULTS Overall, 7457 children were enrolled in the PEER, for a total of 26,792 person-years. Children used a mean (SD) of 793 (1356) g of pimecrolimus when enrolled in the study. As of May 2014, five malignancies had been reported. These include 2 leukemias, 1 osteosarcoma, and 2 lymphomas. No skin cancers were reported. The standardized incidence ratio for all malignancies (primary outcome) based on the age-standardized SEER population was 1.2 (95% CI, 0.5-2.8). As secondary analyses, the standardized incidence ratios (based on 2 cases for each) were 2.9 (95% CI, 0.7-11.7) for lymphoma and 2.0 (95% CI, 0.5-8.2) for leukemia. None of these findings were statistically significant. CONCLUSIONS AND RELEVANCE Based on more than 25,000 person-years of follow-up, it seems unlikely that topical pimecrolimus as it was used in the PEER cohort to treat atopic dermatitis is associated with an increased risk of malignancy.
A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs

Recently, a number of researchers have investigated a class of graph partitioning algorithms that reduce the size of the graph by collapsing vertices and edges, partition the smaller graph, and then uncoarsen it to construct a partition for the original graph [Bui and Jones, Proc. of the 6th SIAM Conference on Parallel Processing for Scientific Computing, 1993, 445--452; Hendrickson and Leland, A Multilevel Algorithm for Partitioning Graphs, Tech. report SAND 93-1301, Sandia National Laboratories, Albuquerque, NM, 1993]. From the early work it was clear that multilevel techniques held great promise; however, it was not known if they can be made to consistently produce high quality partitions for graphs arising in a wide range of application domains. We investigate the effectiveness of many different choices for all three phases: coarsening, partition of the coarsest graph, and refinement. In particular, we present a new coarsening heuristic (called heavy-edge heuristic) for which the size of the partition of the coarse graph is within a small factor of the size of the final partition obtained after multilevel refinement. We also present a much faster variation of the Kernighan--Lin (KL) algorithm for refining during uncoarsening. We test our scheme on a large number of graphs arising in various domains including finite element methods, linear programming, VLSI, and transportation. Our experiments show that our scheme produces partitions that are consistently better than those produced by spectral partitioning schemes in substantially smaller time. Also, when our scheme is used to compute fill-reducing orderings for sparse matrices, it produces orderings that have substantially smaller fill than the widely used multiple minimum degree algorithm.