Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening candidate microR-15a- IRAK2 regulatory pairs for predicting the response to Staphylococcus aureus-induced mastitis in dairy cows

Abstract We established a mastitis model using exogenous infection of the mammary gland of Chinese Holstein cows with Staphylococcus aureus and extracted total RNA from S. aureus-infected and healthy mammary quarters. Differential expression of genes due to mastitis was evaluated using Affymetrix technology and results revealed a total of 1230 differentially expressed mRNAs. A subset of affected genes was verified via Q-PCR and pathway analysis. In addition, Solexa high-throughput sequencing technology was used to analyze profiles of miRNA in infected and healthy quarters. These analyses revealed a total of 52 differentially expressed miRNAs. A subset of those results was verified via Q-PCR. Bioinformatics techniques were used to predict and analyze the correlations among differentially expressed miRNA and mRNA. Results revealed a total of 329 pairs of negatively associated miRNA/mRNA, with 31 upregulated pairs of mRNA and 298 downregulated pairs of mRNA. Differential expression of miR-15a and interleukin-1 receptor-associated kinase-like 2 (IRAK2), were evaluated by western blot and luciferase reporter assays. We conclude that miR-15a and miR-15a target genes (IRAK2) constitute potential miRNA–mRNA regulatory pairs for use as biomarkers to predict a mastitis response.
Endoplasmic reticulum stress differentially inhibits endoplasmic reticulum and inner nuclear membrane protein quality control degradation pathways

Endoplasmic reticulum (ER) stress occurs when the abundance of unfolded proteins in the ER exceeds the capacity of the folding machinery. Despite the expanding cadre of characterized cellular adaptations to ER stress, knowledge of the effects of ER stress on cellular physiology remains incomplete. We investigated the impact of ER stress on ER and inner nuclear membrane protein quality control mechanisms in Saccharomyces cerevisiae. We analyzed the turnover of substrates of four ubiquitin ligases (Doa10, Rkr1/Ltn1, Hrd1, and the Asi complex) and the metalloprotease Ste24 in induced models of ER stress. ER stress did not substantially impact Doa10 or Rkr1 substrates. However, Hrd1-mediated destruction of a protein that aberrantly engages the translocon (Deg1-Sec62) and substrates with luminal degradation signals was markedly impaired by ER stress; by contrast, Hrd1-dependent degradation of proteins with intramembrane degrons was largely unperturbed by ER stress. ER stress impaired the degradation of one of two Asi substrates analyzed and caused a translocon-clogging Ste24 substrate to accumulate in a form consistent with persistent translocon occupation. Degradation of Deg1-Sec62 in the absence of stress and stabilization during ER stress were independent of four ER stress–sensing pathways. Our results indicate ER stress differentially impacts degradation of protein quality control substrates, including those mediated by the same ubiquitin ligase. These observations suggest the existence of additional regulatory mechanisms dictating substrate selection during ER stress.
Temporal Discrimination is Altered in Patients With Isolated Asymmetric and Jerky Upper Limb Tremor

Unilateral or very asymmetric upper limb tremors with a jerky appearance are poorly investigated. Their clinical classification is an unsolved problem because their classification as essential tremor versus dystonic tremor is uncertain. To avoid misclassification as essential tremor or premature classification as dystonic tremor, the term indeterminate tremor was suggested.
The spirituality index of well-being: Development and testing of a new measure

From the Department of Family Medicine (T.P.D.) and the Center on Aging (T.P.D.), (S.A.S.), University of Kansas Medical Center, Kansas City, KS; Psychology and Research in Education, School of Education, University of Kansas, Lawrence, KS (B.B.F.); and Rho Inc., Chapel Hill, NC (D.W.). This study was supported by the Robert Wood Johnson Foundation Generalist Physician Faculty Scholars Program (T.P.D.), the John A. Hartford Foundation (T.P.D.), Merck Research Laboratories (D.W., S.A.S.), and the Kansas Claude D. Pepper Older Americans Independence Center (AG 14635; D.W., S.A.S.). This work was presented at the Annual Meeting of the North American Primary Care Research Group; November 5, 2000; Amelia Island, FL; and the Annual Meeting of the American Geriatrics Society; May 11, 2001; Chicago, IL.
Breast Cancer Screening in Women With Schizophrenia: A Systematic Review and Meta-Analysis.

OBJECTIVE Women with schizophrenia appear to receive breast cancer diagnoses at later stages of the disease compared with the general population. To study this disparity, this report reviewed and quantified the differences in rates of mammography screening for women with schizophrenia and other psychotic disorders compared with the general population. METHODS A systematic literature search was conducted in PubMed, Embase, Web of Science, and PsycINFO databases. Each database was searched from inception to September 14, 2018. The search strategy included search terms for breast cancer, mammography, schizophrenia, and psychosis. Two reviewers independently screened and evaluated eligible studies. The main outcome measure was the rate of mammography screening among women with schizophrenia and psychotic disorders versus a comparable population of women without these diagnoses. Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were used for abstracting data, and the Newcastle-Ottawa Scale was used for assessing data quality. A meta-analysis with a random-effects model was performed. RESULTS From a total of 304 abstracts reviewed, 11 studies met the inclusion criteria, representing 25,447 women with diagnoses of schizophrenia or psychosis across four countries. The meta-analysis showed that women with schizophrenia were less likely than women without schizophrenia to receive mammography screening (pooled OR=0.50, 95% confidence interval=0.38-0.64, p<0.001). In subgroup analysis, this association was not significantly affected by quality of the study. CONCLUSIONS Women with schizophrenia and other psychotic disorders were about half as likely as the general population to receive mammography screening. Further research is needed to determine causes of this disparity.
Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy

Abstract The features of previously unexplored labile complexes of human 40S ribosomal subunits with RNAs, whose formation is manifested in the cross-linking of aldehyde derivatives of RNAs to the ribosomal protein uS3 through its peptide 55–64 located outside the mRNA channel, were studied by EPR spectroscopy methods. Analysis of subatomic 40S subunit models showed that a likely site for labile RNA binding is a cluster of positively charged amino acid residues between the mRNA entry site and uS3 peptide 55–64. This is consistent with our finding that the 3′-terminal mRNA fragment hanging outside the 40S subunit prevents the cross-linking of an RNA derivative to this peptide. To detect labile complexes of 40S subunits with RNA by DEER/PELDOR spectroscopy, an undecaribonucleotide derivative with nitroxide spin labels at terminal nucleotides was utilized. We demonstrated that the 40S subunit channel occupancy with mRNA does not affect the RNA derivative binding and that uS3 peptide 55–64 is not involved in binding interactions. Replacing the RNA derivative with a DNA one revealed the importance of ribose 2′-OH groups for the complex formation. Using the single-label RNA derivatives, the distance between the mRNA entry site and the loosely bound RNA site on the 40S subunit was estimated.
Long noncoding RNA 91H overexpression contributes to the growth and metastasis of HCC by epigenetically positively regulating IGF2 expression

Long noncoding RNA 91H is transcribed from the H19/IGF2 locus and contributes to the development of breast and oesophagus cancers by regulating the expression of IGF2, but the regulation mechanism remains poorly characterized. Here, we explored the role of 91H in hepatocellular carcinoma (HCC) and the mechanism of IGF2 expression regulation by 91H.
Let-7e Suppresses DNA Damage Repair and Sensitizes Ovarian Cancer to Cisplatin through Targeting PARP1

Increased DNA damage repair is one of the mechanisms implicated in cisplatin resistance. Our previous study indicated that the deregulation of let-7e promoted cisplatin resistance and that let-7e could suppress DNA double-strand break repair in ovarian cancer. In this study, we further characterized the role of let-7e in DNA damage repair and cisplatin resistance in ovarian cancer, and investigated the underlying mechanisms. The alkaline and neutral comet assay indicated that let-7e impeded both DNA single- and double-strand break repairs through downregulating its target gene PARP1. In vitro and in vivo experiments provided evidence that the let-7e–PARP1–DNA repair axis was involved in the modulation of cisplatin sensitivity in ovarian cancer. Contrary to let-7e, PARP1 was overexpressed in cisplatin-resistant ovarian cancer tissues, and patients with high PARP1 expression exhibited poor progression-free survival (PFS) and overall survival (OS). Multivariate logistic and Cox regression analyses showed that let-7e and FIGO stage were independent prognostic factors for PFS and OS, whereas let-7e and PARP1 were able to independently predict chemotherapy response. Taken together, our results indicated that low expression of let-7e promoted DNA single- and double-strand break repairs and subsequently contributed to cisplatin resistance by relieving the suppression on PARP1 in ovarian cancer. Implications: Targeting the let-7e–PARP1–DNA repair axis might be an effective strategy for the treatment of chemoresistant ovarian cancer.
Aphids of the family Adelgidae in Lithuania: distribution, host specificity and molecular (mitochondrial COI and nuclear EF-1α) diversity

Based on the original research of 2017–2018, also reference data, four aphid species and five species complexes of the family Adelgidae listed for Lithuanian fauna. Pineus (Pineus) strobi (Hartig, 1839) is a new species for the fauna of Lithuania. Summarized information on the distribution and host specificity of adelgid species in Lithuania is presented. The most common species recorded from all geographical regions of Lithuania were the ones belonging to the species complexes Adelges laricis – A. tardus, Pineus orientalis – P. pini, Sacchiphantes viridis – S. abietis and Gilletteella cooleyi – G. coweni. Six species of Adelgidae inhabit host plants of the genus Picea, three live on Larix, three – on Pinus, two – on Abies, one – on Pseudotsuga. Partial sequences of mitochondrial (COI) and nuclear (EF-1α) DNA of Lithuanian samples were analysed in comparison with available data from GeneBank representing samples from Central Europe. Pairwise distances of COI and EF-1α fragments between samples belonging to species complexes Adelges laricis – A. tardus, Dreyfusia nordmannianae – D. piceae, Sacchiphantes viridis – S. abietis, Gilletteella cooleyi – G. coweni and Pineus orientalis – P. pini suggest each species complex being a single species.
Original article: Treatment outcome in Hodgkin's disease in patients above the age of 60: A population-based study

Summary All persons in three Swedish counties afflicted with Hodgkin's disease between 1979 and 1988 were traced. The objective was to analyze, in unselected, population-based material, whether an assumed worse prognosis in the elderly could be due to differences in staging procedures, treatment intensity, decreased tolerance to therapy or to a more aggressive disease. After histopathologjcal revision, 163 of 202 patients (autopsy cases excluded) were accepted as HD, 61 (37%) of them above the age of 60. Although staging procedures had been more intense in the young, the elderly patients had a more advanced stage at diagnosis, and tended more often to have B-symptoms. The intensity of staging procedures did not seem to influence survived. The 5-yr relative survival was 37% above and 85% below the age of 60. Radiotherapy was the primary treatment in 12 (20%) above and 41 (41%) below the age of 60 with 5-yr relative survival figures of 84% and 85%, respectively. Thirty-seven patients (61%) above and 61 (59%) below 60 were treated with combination chemotherapy (MOPP/ABVD, MOPP, ChlVPP/OPEC) with curative intent. The 5-yr relative survival was 33% and 86%, respectively. The majority of the elderly patients (54%) received less than 40% of the planned chemotherapy dose. The main reason for this pronounced reduction was intolerance to therapy, with 8 treatment-related deaths. We conclude that tolerance to combination chemotherapy in the elderly patients with HD is poor and could be the major reason for poor treatment outcome in this age group.
Biological approach in nanobiotechnology – screening of four food pathogenic bacteria extract ability in extracellular biosynthesis of gold nanoparticles

Gold nanoparticles (Au NPs) were hydrothermally synthesized at 121 °C and 1.5 bar for 15 min, using four foodborne pathogens extracts namely, Bacillus cereus , Escherichia coli , Staphylococcus aureus and Salmonella entericasubsp.enterica . Fourier transform infrared spectroscopy indicated that hydroxyl and amide groups were two main functional groups which those were existed in all provided bacterial extracts and had key roles in the reduction and stabilizing processes. Particle size, polydispersity index (PDI), zeta potential, broad emission peak (λ max ) and concentration of fabricated Au NPs were assessed using UV-Vis spectrophotometer and dynamic light scattering (DLS) particle size analyzer. Results indicated that, synthesized Au NPs using S. aureus had minimum particle size (51.11 nm) and PDI (0.599), with zeta potential value of 15.3 mV, and concentration (0.04 ppm) values, which were more desirable as compared to those of synthesized Au NPs using other three bacterial extracts.
Teenagers' Experience with Occupational Health and Safety Issues in West Virginia

Students in three high schools in West Virginia completed one of three questionnaires according to work status. A total of 1156, 14- to 17-year-old students completed the survey, 17% had ever (currently or previously) worked. These students reported employment mostly during June to August (36%), mainly in recreational facilities (15%). The main task performed was cleaning (44%). Forty-five percent experienced one or more on-the-job injuries with cuts being the most common. A large number of the teenagers (84%) reported receiving training in how to do their job and little training on safety and health. When the teenagers were queried on who is at fault when a teenager is injured, 46% indicated that accidents just happen and 38% blamed the teenager. The respondents indicated they had used scaffolding and ladders (32%), power tools (29%), and/or driven mo tor vehicle (15%), all tasks prohibited by child labor laws. The results indicate a deficiency in knowledge among this group of teenagers on topics related to occupational safety and health and child labor laws. A need exists for a concerted team approach to address these problems.
Screening for Multidrug Resistance Bacteria Pseudomonas Aeruginosa in Hospitalized Patient in Hosur, Krishnagiri (DT)

Pseudomonas aeruginosa is a classic opportunistic pathogen because of its innate resistance to many antibiotics and disinfectants. It is also the most common Gram negative bacterium found in nosocomial infections causing various spectra of infections especially in neutropenic, immunocompromised, burns / tissue injury and cystic fibrosis patients all over the world. Recent advances in medicine such as the advent of more elaborate surgery and intensive care, the use of immunosuppressive drugs, the availability of invasive procedures and the increase in number of immunocompromised patients means there is a rise in patients with impaired immune defences liable to nosocomial infections. The increasing incidence of infections caused by multidrug resistant organisms have caused attention to be focused on measures for fighting resistance, foremost of which is susceptibility surveillance . This study therefore determined the prevalence, antibiotic susceptibility and resistant patterns of Pseudomonas aeruginosa strains from clinical specimens.
Book Review A. Darwiche, Modeling and Reasoning with Bayesian Networks, Cambridge, 2009

The field of probabilistic reasoning with Bayesian networks has experienced fruitful advancement in the last three decades, generating a large body of rich literature. Beginning with Pearl’s influential 1988 book, there have been now over a dozen books that cover the diverse topics in this field. These books, successively published over a two-decade period, cover the latest development of the field at the time of the writing. Furthermore, as the field sufficiently matures to have a broader impact on AI practice, it is necessary to make the key results more accessible to a broader audience beyond researchers specialized in the field. As a result, newly published books increasingly appeal better to a wider readership. The book Modeling and Reasoning with Bayesian Networks by Adnan Darwiche is an excellent example of this trend. The book provides a comprehensive, accessible and advanced treatment of the representational and computational issues surrounding probabilistic reasoning with Bayesian Networks. Adnan Darwiche is a leading researcher and is responsible for a number of techniques presented in the book. The book contains eighteen chapters which can be partitioned, in my opinion, into six groups according to their topics, although Darwiche makes no such partition. Chapters in each group are not necessarily adjacent in the book.
Multiscalar processors

Multiscalar processors use a new, aggressive implementation paradigm for extracting large quantities of instruction level parallelism from ordinary high level language programs. A single program is divided into a collection of tasks by a combination of software and hardware. The tasks are distributed to a number of parallel processing units which reside within a processor complex. Each of these units fetches and executes instructions belonging to its assigned task. The appearance of a single logical register file is maintained with a copy in each parallel processing unit. Register results are dynamically routed among the many parallel processing units with the help of compiler-generated masks. Memory accesses may occur speculatively without knowledge of preceding loads or stores. Addresses are disambiguated dynamically, many in parallel, and processing waits only for true data dependences. This paper presents the philosophy of the multiscalar paradigm, the structure of multiscalar programs, and the hardware architecture of a multiscalar processor. The paper also discusses performance issues in the multiscalar model, and compares the multiscalar paradigm with other paradigms. Experimental results evaluating the performance of a sample of multiscalar organizations are also presented.
Use of viewpoint planning for fast succinct map matching

Map matching, the ability to match a local map built by a mobile robot to previously built maps, is crucial in robot vision applications. In this paper, we propose a novel map descriptor, to facilitate fast succinct text-based map matching. Unlike previous bag-of-words approaches that trade discriminativity for viewpoint invariance, we develop a holistic view descriptor that is view-dependent and highly discriminative. Because the success of our holistic view descriptor depends on the assumption that the viewpoint is unique given a local map, we also address the issue of viewpoint planning and present a solution that provides similar views for similar local maps. The results of experiments conducted verify the efficacy of our proposed approach.
Studies on variability and character association in ashwagandha [Withania somnifera (L.) Dunal]

Ashwagandha [Withania somnifera (L.) Dunal] is an important medicinal plant which is major source of alkaloids, viz., withanine, sominiferine, sominiferinine, somnine, withananine and withasomnine. The genetic variability, correlation and path analysis of dry root yield and its contributing traits were analyzed in twenty seven diverse genotypes of Ashwagandha. The highest magnitude of genotypic and phenotypic coefficient of variation was recorded for number of primary branches per plant. The heightest heritability was coupled with high genetic gain was recorded for total alkaloid content, which indicated the importance of additive gene effect, which could be therefore improved through selection. The plant height positively correlated with dry root yield and root diameter but negatively correlated with days to 75% maturity. Among the characters, maximum direct effect was recorded for plant height followed by total alkaloid content. Superior genotypes, viz., MPAS-6, MPAS-4, MPAS-10, MPAS-5, and MPAS-1 could be gainfully utilized in the improvement of dry root yield in Ashwagandha.
Probabilistic Multiknob High-Level Synthesis Design Space Exploration Acceleration

One of the biggest advantages of C-based very large scale integration design over traditional register transfer level is its ability to automatically generate architectures with different area versus performance characteristics without the need of modifying the original behavioral description. Different knobs can be explored to obtain the dominating tradeoff curve (Pareto-front). So far previous works have only focused on exploring one set of knobs or combining all of them together without considering the underlying implications of each of these knobs. This paper presents the first method that accelerates the design space exploration (DSE) by first classifying these knobs and exploring them sequentially, thus reducing the design space to be explored considerably. In particular: 1) local synthesis directives in the form of pragmas inserted directly at the source code and 2) functional units (FUs) number and type. Second, we propose a probabilistic method to further accelerate the DSE by computing the probability of each micro-architecture generated after the pragma exploration stage, to lead to new dominating designs and in turn exploring only those with the highest probabilities. One additional contribution is that the explorer for both knobs are implemented using novel heuristics. The pragma based explorer is based on ant colony optimization, while the FU explorer explores the number and type of FUs in order to further maximize the total amount of resource sharing that can be extracted. Experimental results show that our proposed method finds Pareto-fronts of similar quality than an exploration method optimized for quality of their results, while accelerating the DSE by an average of $12.2 {\times }$ .