Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of the FMR1 mutation in Taiwan assessed by large‐scale screening of newborn boys and analysis of DXS548‐FRAXAC1 haplotype

If carrier women could be identified in time and take appropriate measures, fragile X syndrome (FXS) can be prevented. Wide screening of women to be or in their early pregnancy was considered a good approach to identify carriers without misdetection. Nevertheless, we argued against the cost‐effectiveness of implementing such a screening program in Taiwan, due to the lower carrier rate found in our pilot study. To reliably estimate the prevalence of mutant FMR1 gene in Taiwan, we anonymously screened 10,046 newborn boys using bloodspot polymerase chain reaction (PCR). Among them, the sample from one boy, who was most likely had FXS, failed repeatedly in PCR amplification. The estimated prevalence of premutation (55–200 CGG repeats) and intermediate alleles (45–54 CGG repeats) was 1:1,674 (n = 6) and 1:143 (n = 70), respectively. All these estimates were constantly lower than that reported in Caucasian populations, with variable statistic significance. Furthermore, when comparing analyses of the distribution of alleles at the two most often investigated microsatellite loci, DXS548 and FRAXAC1, between 100 control and 28 unrelated fragile X chromosomes, we found no apparent founder haplotype prevalent among the fragile X patients. Because a few founder haplotypes were reportedly prevalent in two thirds of fragile X alleles in Caucasians and in Chinese from Central China, we thus suggested that lack of founder fragile X chromosomes might result in a relatively low prevalence of mutant FMR1 gene in a population, as observed in Taiwan. © 2005 Wiley‐Liss, Inc.
Joint virtual machine placement and migration scheme for datacenters

Efficiently managing virtual machines (VMs) plays a key role in improving the resource usage and power consumption of datacenters. However, most of the existing techniques have been optimized for each system criterion separately (e.g., either platform layer or virtualization layer). Such approaches are simple to implement, but they usually result in poor system performance or under-utilization of the resources. In this paper, we investigate the problem of optimal VM management (i.e., placement and migration) in datacenters via a multi-objective function. We show that optimizing the proposed multi-objective function reduces not only the energy consumption, but also the cross network traffic among platforms. Due to the high complexity of the combinatorial optimization problem, we propose an efficient heuristic algorithm to find a near optimal solution based on the relaxed convex optimization framework. We provide both theoretical analysis and simulations to show the effectiveness of the proposed approach over the existing approaches.
Two-Sided Matching: A Study in Game-Theoretic Modeling and Analysis

Foreword Robert Auman Acknowledgment 1. Introduction Part I. One-To-One Matching: the Marriage Model: 2. Stable matchings 3. The structure of the set of stable matchings 4. Strategic questions Part II. Many-To-One Matching: Models in which Firms May Employ Many Workers: 5. The college admissions model and the labor market for medical interns 6. Discrete models with money, and more complex preferences Part III. Models of One-To-One Matching with Money as a Continuous Variable: 7. A simple model of one seller and many buyers 8. The assignment game 9. The generalization of the assignment model Part IV. Epilogue: 10. Open questions and research directions Bibliography Indexes.
Genotype—environment interactions and the estimation of the genomic mutation rate in Drosophila melanogaster

We have studied the relative fitnesses of three genotypes of Drosophila melanogaster in 50 environments. Two genotypes, the MA lines, had accumulated mutations in the absence of natural selection over 62 generations. The third was a related strain where selection had continued to act. The environments differed in three factors: parental density, dilution of the medium, and the temperature ré⁪gime and medium composition. Our measure of fitness assessed fecundity and viability relative to a reference genotype. Both MA lines always had lower fitnesses than the selected line, but the difference increased dramatically with dilution of the medium and, especially, crowding. Under the most severe conditions, the performance of the MA lines approached 0. This increased difference in harsh conditions may be caused both by a uniform increase in the magnitude of deleterious effects of all mutations and by the exposure of mutations which are essentially neutral under benign conditions. If the second cause is important, previous experiments are likely to have underestimated the genomic deleterious mutation rate in Drosophila melanogaster more than previously thought.
Protracted Conflicts and Rehabilitation

Conflict in different hues has been a recurrent feature of the human society. These sometimes escalate and become violent. Violent conflict amongst social groups inflicts deep wounds and scars on the society that endures it. Apart from the deaths and destruction it causes, it fragments the social structure and fabric of the society that suffers it. There is an enormous impact on the economy that results in stunted growth and development. Some societies are so severely destabilised that they take many generations to recover from its trauma. African leaders for example have stated that the ‘continued prevalence of armed conflicts in Africa and the fact that no single internal factor has contributed more to socio-economic decline of the Continent and the suffering of the civilian population than the scourge of conflicts within and between states’ (African Union, 2002).
Predictive Performance of Placental Protein 13 for Screening Preeclampsia in the First Trimester: A Systematic Review and Meta-Analysis

Preeclampsia is a pregnancy-specific syndrome that affects maternal and neonatal mortality. Several serum biomarkers can be used to predict preeclampsia. Among these proteins, placental protein 13 (PP13) has received progressively more interest in recent studies. The decrease in PP13 expression is one of the earliest signs for the development of preeclampsia and has shown its predictive performance for preeclampsia. In this meta-analysis, we collected 17 observational studies with 40,474 pregnant women. The overall sensitivity of PP13 to predict preeclampsia was 0.62 [95% confidence interval (CI) = 0.49–0.74], the specificity was 0.84 (95%CI = 0.81–0.86), and the diagnostic odds ratio was nine (95%CI = 5–15). The area under the curve for summary receiver operating characteristic was 0.84. We then chose the early-onset preeclampsia as a subgroup. The sensitivity of early-onset subgroup was 0.63 (95%CI = 0.58–0.76), the specificity was 0.85 (95%CI = 0.82–0.88), and the diagnostic odds ratio was 10 (95%CI = 6–18). The findings of our meta-analysis indicate that PP13 may be an effective serum biomarker for the predictive screening of preeclampsia. Nonetheless, large prospective cohort studies and randomized controlled trials are expected to uncover its application in clinical practice. The heterogeneity of the original trials may limit the clinical application of PP13. Systematic Review Registration: https://www.crd. york.ac. uk/PROSPERO/display_record. php? RecordID=188948 The meta-analysis was registered in PROSPERO (CRD42020188948).
Design of a Seven-Genome Escherichia coli Microarray for Comparative Genomic Profiling

ABSTRACT We describe the design and evaluate the use of a high-density oligonucleotide microarray covering seven sequenced Escherichia coli genomes in addition to several sequenced E. coli plasmids, bacteriophages, pathogenicity islands, and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 (Δstx 2::cat) as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. By using fluorescently labeled genomic DNA to query the microarrays and subsequently analyze common virulence genes and phage elements and perform whole-genome comparisons, we observed that O175:H16 D1 is a K-12-like strain and confirmed that its φ3538 (Δstx 2::cat) phage element originated from the E. coli 3538 (Δstx 2::cat) strain, with which it shares a substantial proportion of phage elements. Moreover, a number of genes involved in DNA transfer and recombination was identified in both new strains, providing a likely explanation for their capability to transfer φ3538 (Δstx 2::cat) between them. Analyses of control samples demonstrated that results using our custom-designed microarray were representative of the true biology, e.g., by confirming the presence of all known chromosomal phage elements as well as 98.8 and 97.7% of queried chromosomal genes for the two control strains. Finally, we demonstrate that use of spatial information, in terms of the physical chromosomal locations of probes, improves the analysis.
Analisis Word2vec untuk Perhitungan Kesamaan Semantik antar Kata

Abstrak Implementasi perhitungan kesamaan semantik antar kata merupakan salah satu tugas yang dapat diselesaikan dalam bidang Natural Language Processing(NLP). Perhitungan kesamaan semantik antar kata dapat digunakan untuk membantu mesin dalam memahami bahasa manusia. Selain itu, perhitungan kesamaan semantik juga dapat digunakan sebagai dasar penelitian tahap selanjutnya pada bidang NLP. Penelitian ini dilatar belakangi oleh suatu masalah dimana pada saat ini pencarian sistem informasi banyak melibatkan teks atau dokumen, namun mesin belum dapat menyamakan persepsi manusia dengan baik sehingga mesin perlu dibantu untuk memahami teks atau dokumen tersebut. Sepasang kata dinyatakan mempunyai kesamaan semantik apabila memiliki kesamaan pada makna atau konsep. Pada penelitian ini, dilakukan implementasi perhitungan kesamaan semantik antar kata untuk bahasa Inggris. Korpus yang digunakan pada penelitian ini yaitu Brown Corpus, Berita Corpus, dan Harry Potter Corpus. Dokumen tersebut diubah kedalam bentuk vektor dengan Word2vec. Selanjutnya nilai kesamaan semantik yang dihasilkan dari vektor tersebut dibandingkan dengan dataset Gold Standard SimLex999 untuk mengukur nilai korelasinya. Hasil pengujian menunjukkan bahwa pengukuran Word2vec menghasilkan korelasi sebesar 0.192 dengan perhitungan korelasi Pearson. Kata kunci : Kesamaan Semantik, Natural Language Processing, Word2vec Abstract The implementation of calculation semantic similarity between word is one of task that can be done by Natural Language Processing. The calculation of semantic similarity between word can used to help the machine to understanding of human language(natural language). Beside that, calculation of semantic similarity can be used as a basic of the next step in NLP’s research. The main idea of this study is motivated by a problem where nowaday the seaarch of information sistem are involved by many text and document, so we need to help the machine to understand those texts or documents. A pair of word are similar if they have similarity to the level of meaning of concept. In this research, we are implement the calculation of semantic similarity between word in English. The corpus that used in this research are Brown Corpus, Berita Corpus, and Harry Potter Corpus. That documents are convert into vector space by using Word2vec. Next, the score of semantic similarity generated by vector are compared to SimLex999 Gold Standard dataset to measure their corelation. The result showed that Word2vec have corelation’s score of 0.192 in Pearson corelation. Keywords: Semantic Similarity, Natural Language Processing, Word2vec
Financial frictions and shock transmission: the Portuguese case

This article uses the PESSOA model to assess the macroeconomic impact of two relevant shocks that conditioned the Portuguese economy in the recent past: the fall in external demand and the rise in sovereign debt risk premium. PESSOA is a general equilibrium model, calibrated to incorporate the main features of the Portuguese economy. The recession driven by the external demand shock is magnified by the prevalence of financial frictions, in particular due to the drop in investment, which does not occur in the case of the risk premium shock. Financial frictions increase the persistence of recessionary effects, especially in the external demand shock, to the extent that capital holders experience a persistent reduction of their net worth, which increases the degree of leverage, the risk levels associated with investment projects, and the costs of external financing. Results show also that the recession causes a decrease in fiscal revenues in both shocks, and thus fiscal policy must take a restrictive stance to ensure the stability of public debt in the medium and long term.
PROTECTIVE EFFECTS OF ISCHEMIC PRECONDITIONING ON THE COLD-PRESERVED LIVER ARE TYROSINE KINASE DEPENDENT

Background. Little data exist regarding the use of ischemic preconditioning before sustained hepatic cold storage. We hypothesized that ischemic preconditioning protects hepatic grafts via a tyrosine kinase–dependent pathway. Methods. Six porcine livers underwent routine harvest (control). Five other livers underwent 15 min of in situ ischemia followed by 15 min of reflow before harvest (ischemic preconditioning). Another five livers were pretreated with a tyrosine kinase inhibitor (genistein) before preconditioning. Upon reperfusion and after 2 hours of cold storage, graft function, graft circulatory impairment, and markers of cellular damage were analyzed. Tissue cytoplasmic extracts were analyzed for tyrosine phosphorylation with Western blot. Significance was determined with t tests. Results. Ischemic-preconditioned grafts demonstrated enhanced bile production, augmented responses to a bile acid challenge, and elevated O2 consumption (P <0.05) compared to controls. Also, preconditioned grafts demonstrated improved hepatic tissue blood flow and decreased hepatic vascular resistance (P <0.005) compared to controls. Endothelial cell preservation (factor VIII immunostain) was improved in preconditioned graft biopsies compared to controls. With genistein pretreatment, all observed improvements returned to control levels. Analysis of cytoplasmic extracts demonstrated an increase in tyrosine phosphorylation before cold ischemia in preconditioned grafts only, but not in control or genistein-pretreated grafts. Conclusions. The data indicate that ischemic preconditioning protects the liver from sustained cold ischemia and that tyrosine kinases are involved in preconditioning responses.
Persistence of Leishmania donovani Antibodies in Past Visceral Leishmaniasis Cases in India

ABSTRACT The persistence of anti-Leishmania donovani antibodies in past visceral leishmaniasis (VL) cases was retrospectively assessed by means of the direct agglutination test (DAT) and the rK39 enzyme-linked immunosorbent assay (ELISA). Antibody titers remained high for an extended period of time in past cases of VL. These results highlight the need to carefully elicit the history of patients with VL symptoms.
Importance of enteric bacteria as a cause of pneumonia, meningitis and septicemia among children in a rural community in The Gambia, West Africa

Two thousand eight hundred ninety-eight children younger than 5 years old were investigated during a 2-year period in a rural area of The Gambia for possible pneumonia, meningitis or septicemia. After clinical examination and appropriate investigations, 1014 children were diagnosed as having pneumonia, 31 as having meningitis and 100 as having septicemia. Nine hundred seven children had a final diagnosis of malaria including 702 who satisfied the World Health Organization criteria for a diagnosis of pneumonia. A bacterial etiology was established in 115 (11%) patients with a final diagnosis of pneumonia, in 25 (81%) with meningitis and in 29 (29%) with suspected septicemia. Overall the
Drosophila Short Neuropeptide F Regulates Food Intake and Body Size*

Neuropeptides regulate a wide range of animal behavior including food consumption, circadian rhythms, and anxiety. Recently, Drosophila neuropeptide F, which is the homolog of the vertebrate neuropeptide Y, was cloned, and the function of Drosophila neuropeptide F in feeding behaviors was well characterized. However, the function of the structurally related short neuropeptide F (sNPF) was unknown. Here, we report the cloning, RNA, and peptide localizations, and functional characterizations of the Drosophila sNPF gene. The sNPF gene encodes the preprotein containing putative RLRF amide peptides and was expressed in the nervous system of late stage embryos and larvae. The embryonic and larval localization of the sNPF peptide in the nervous systems revealed the larval central nervous system neural circuit from the neurons in the brain to thoracic axons and to connective axons in the ventral ganglion. In the adult brain, the sNPF peptide was localized in the medulla and the mushroom body. However, the sNPF peptide was not detected in the gut. The sNPF mRNA and the peptide were expressed during all developmental stages from embryo to adult. From the feeding assay, the gain-of-function sNPF mutants expressed in nervous systems promoted food intake, whereas the loss-of-function mutants suppressed food intake. Also, sNPF overexpression in nervous systems produced bigger and heavier flies. These findings indicate that the sNPF is expressed in the nervous systems to control food intake and regulate body size in Drosophila melanogaster.
Promoters for synthesis of the pre-C and pregenomic mRNAs of human hepatitis B virus are genetically distinct and differentially regulated

Two similar, yet functionally distinct genomic RNAs are transcribed from the DNA genome of the human hepatitis B virus. The pre-C RNAs encode the precore protein which is proteolytically processed to yield e antigen. The pregenomic RNAs encode both the nucleocapsid protein and reverse transcriptase and serve as the templates for viral DNA replication. To determine whether synthesis of these two RNAs is directed from a single or a closely spaced pair of promoters, we introduced point and insertion mutations into the basal elements of the promoter that directs their synthesis. Transcription from these mutants was examined both in cell-free transcription systems derived from hepatoma (HepG2) and nonliver (HeLa) cell lines and by transient transfection of hepatoma cell lines (Huh7 and HepG2). The data from these experiments indicated that synthesis of the pre-C and pregenomic RNAs is directed by two distinct promoters and that the basal elements of these two promoters partially overlap, yet are genetically separable, with each consisting of its own transcriptional initiator and a TATA box-like sequence situated approximately 25 to 30 bp upstream of its sites of initiation. A 15-bp insertion was found to be sufficient to physically separate these two promoters. Furthermore, these two promoters can be differentially regulated, with the transcriptional activator Sp1 specifically activating transcription from the pregenomic promoter and the hepatocyte nuclear factor 4 specifically repressing transcription from the pre-C promoter. Thus, we conclude that the promoters used in synthesis of the pre-C and pregenomic mRNAs are genetically distinct and separately regulated.
Optimal monetary policy in an independent world

In the literature on international monetary policy, the paradigm is that gains from coordination are fairly small. Monetary policy is conducted to stabilize macroeconomic fluctuations and gains from policy coordination arise from preventing national monetary authorities from strategically manipulating the terms of trade by means of these stabilization policy instruments. However, as it has been emphasized by Lucas (2003), welfare gains from stabilizing fluctuations are generically small since they are of second order. In this paper, I develop a dynamic stochastic two-country model with sticky wages and a cash-in-advance restriction which is in the spirit of the New Open Economy Macroeconomics framework. In this environment, monetary authorities can manipulate the terms of trade by conducting a general short-run monetary policy using both the nominal interest rate and the money supply. The money supply affects the terms of trade by altering the nominal exchange rate ex post and it is used in the traditional way so as to stabilize macroeconomic fluctuations. The nominal interest rate affects the terms of trade by changing expected inflation ex ante. Self-oriented national policymakers use the nominal interest rates to raise the terms of trade ex ante. This leads to an inefficient inflation tax whose welfare effects are of first order. Consequently, gains from monetary policy coordination are of first order.
How do customers judge quality in an e-tailer?

Early research in e-commerce projected that online retailing would spiral into a never-ending price war, but recent research has shown that customers are more likely to pay higher prices to online retailers of high quality that they trust. But how do customers evaluate quality in online retailing? What are the specific aspects of an online transaction that customers value and use to distinguish one site from another? The authors explored these issues by surveying customers who had recently engaged in an online retail transaction to determine how they evaluate the quality of their experiences with online retailers. The results demonstrated that customers? perceptions of quality and satisfaction with online purchases depend upon three things: interaction with the Web site, delivery of the product and how prepared retailers are to address problems when they occur. Of the three, product delivery has the strongest influence on customers? satisfaction and future purchase intentions. The authors further break down each of the three aspects of quality to create a complete picture of what it takes to build a trusting relationship with customers in an e-commerce environment.
Structural Characterization of Clusterin-Chaperone Client Protein Complexes*

Clusterin (CLU) is a potent extracellular chaperone that inhibits protein aggregation and precipitation otherwise caused by physical or chemical stresses (e.g. heat, reduction). This action involves CLU forming soluble high molecular weight (HMW) complexes with the client protein. Other than their unquantified large size, the physical characteristics of these complexes were previously unknown. In this study, HMW CLU-citrate synthase (CS), HMW CLU-fibrinogen (FGN), and HMW CLU-glutathione S-transferase (GST) complexes were generated in vitro, and their structures studied using size exclusion chromatography (SEC), ELISA, SDS-PAGE, dynamic light scattering (DLS), bisANS fluorescence, and circular dichroism spectrophotometry (CD). Densitometry of Coomassie Blue-stained SDS-PAGE gels indicated that all three HMW CLU-client protein complexes had an approximate mass ratio of 1:2 (CLU:client protein). SEC indicated that all three clients formed complexes with CLU ≥ 4 × 107 Da; however, DLS estimated HMW CLU-FGN to have a diameter of 108.57 ± 18.09 nm, while HMW CLU-CS and HMW CLU-GST were smaller with estimated diameters of 51.06 ± 6.87 nm and 52.61 ± 7.71 nm, respectively. Measurements of bisANS fluorescence suggest that the chaperone action of CLU involves preventing the exposure to aqueous solvent of hydrophobic regions that are normally exposed by the client protein during heat-induced unfolding. CD analysis indicated that, depending on the individual client protein, CLU may interact with a variety of intermediates on protein unfolding pathways with different amounts of native secondary structure. In vivo, soluble complexes like those studied here are likely to serve as vehicles to dispose of otherwise dangerous aggregation-prone misfolded extracellular proteins.