Miracle-dz/UniFAR-FTUs huggingface dataset:
FINE MAPPING OF MILK YIELD QTL ON CHROMOSOMES 6 AND 20 IN GERMAN HOLSTEIN POPULATION USING MICROSATELLITE MARKERS

In German Holstein population a very signifi cant QTL with effects on milk yield trait (MY) was mapped on chromosome 6 and 20 to the interval BM143–ILSTS97 and AGLA29–ILSTS72, respectively. Where, three markers BM143, FBN13 and ILSTS97 on chromosome 6 and two markers AGLA29 and ILSTS72 on chromosome 20 were associated with highly signifi cant effects (P<0.01) for milk yield. Findings from this study could be used in subsequent fine-mapping work and applied to marker-assisted selection (MAS) of dairy production traits.
A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing

Both paramutation and Mutator (Mu) transposon inactivation involve heritable changes in gene expression without concomitant changes in DNA sequence. The mechanisms by which these shifts in gene activity are achieved are unknown. Here we present evidence that these two phenomena are linked mechanistically. We show that mutation of a gene, modifier of paramutation 1 (mop1), which prevents paramutation at three different loci in maize, can reverse methylation of Mutator elements reliably. In mop1 mutant backgrounds, methylation of nonautonomous Mu elements can be reversed even in the absence of the regulatory MuDR element. Previously silenced MuDR elements are reactivated sporadically after multiple generations of exposure to mop1 mutations. MuDR methylation is separable from MuDR silencing, because removal of methylation does not cause immediate reactivation. The mop1 mutation does not alter the methylation of certain other transposable elements including those just upstream of a paramutable b1 gene. Our results suggest that the mop1 gene acts on a subset of epigenetically regulated sequences in the maize genome and paramutation and Mu element methylation require a common factor, which we hypothesize influences chromatin structure.
A Cash Flow Based Multi-period Credit Risk Model

Many credit risk models have been proposed in the literature. According to the ir assumptions and emphases, they can be roughly grouped into two categories, “structural-form" models and “reduced-form” models. The former focuses on constructing the distribution of asset values and then estimating one-period probability of default and recovery rate; the latter relies on exogenous information such as credit rating and recovery rate which are not related to asset values. Within the frameworks of the above two categories, few studies use stochastic cash flow model to assess firm’s credit risk. Based upon the two significant cash flow characteristics- “mean-reversion” and “allowing positive or negative values” and the concept of varying coefficient model, the study develops a “ Time-dependent stochastic cash flow model”. To consider future industrial economic state changes’ impacts on a firm’s cash flow, we also construct a stochastic model of industrial economic state. The information forecasted from the state model is used as the base for adjusting the parameters of the time-dependent cash flow model. To perform a multi -period firm valuation, this cash flow model needs only publicly available information of corporate finance and the industrial economic state (i.e. the industrial cyclicality information). With the information of a firm’s value and debt, a “Cash Flow Based Multi-period Credit Risk Model” can be built. We can then price the corporate debt by combining the expected recovery rate generated from our model and the concept of defaultable bond pricing of Jarrow-Turnbull Model (1995).
A 90-Day Tenofovir Reservoir Intravaginal Ring for Mucosal HIV Prophylaxis

ABSTRACT A vaginal gel containing the antiretroviral tenofovir (TFV) recently demonstrated 39% protection against HIV infection in women. We designed and evaluated a novel reservoir TFV intravaginal ring (IVR) to potentially improve product effectiveness by providing a more controlled and sustained vaginal dose to maintain cervicovaginal concentrations. Polyurethane tubing of various hydrophilicities was filled with a high-density TFV/glycerol/water semisolid paste and then end-sealed to create IVRs. In vitro, TFV release increased with polyurethane hydrophilicity, with 35 weight percent water-swelling polyurethane IVRs achieving an approximately 10-mg/day release for 90 days with mechanical stiffness similar to that of the commercially available NuvaRing. This design was evaluated in two 90-day in vivo sheep studies for TFV pharmacokinetics and safety. Overall, TFV vaginal tissue, vaginal fluid, and plasma levels were relatively time independent over the 90-day duration at approximately 104 ng/g, 106 ng/g, and 101 ng/ml, respectively, near or exceeding the highest observed concentrations in a TFV 1% gel control group. TFV vaginal fluid concentrations were approximately 1,000-fold greater than levels shown to provide significant protection in women using the TFV 1% gel. There were no toxicological findings following placebo and TFV IVR treatment for 28 or 90 days, although slight to moderate increases in inflammatory infiltrates in the vaginal epithelia were observed in these animals compared to naïve animals. In summary, the controlled release of TFV from this reservoir IVR provided elevated sheep vaginal concentrations for 90 days to merit its further evaluation as an HIV prophylactic.
Genotoxicity of total and fractionated extractable organic matter in fine air particulate matter from urban Guangzhou: Comparison between haze and nonhaze episodes

To investigate the genotoxic potencies of extractable organic matter (EOM) in aerosols, fine air particulate matter (PM2.5) was collected simultaneously at a roadside (1.2 m above ground) and at a rooftop location (50 m above ground) in urban Guangzhou (China) during a nonhaze period in September 2006 and a haze period in October 2006. Particle‐bound organics were extracted and separated into aliphatic, aromatic, and polar fractions. The genotoxicity of total and fractionated extracts were tested by single‐cell electrophoresis (comet assay) with human blood lymphocytes. The PM2.5 concentrations usually exceeded the U.S. National Ambient Air‐Quality Standard level (65 μg/m3) at both the roadside and the rooftop. During nonhaze days, the roadside samples showed substantially higher PM2.5 levels (108–130 μg/m3) and significantly higher genotoxic effects of total and fractionated EOM (p < 0.05 for >10 m3 air equivalent/ml) than the rooftop samples. During haze days, however, PM2.5 levels and genotoxic potencies of rooftop samples were drastically elevated and comparable to those of roadside samples, implying that during haze episodes, most people in the urban area are exposed to PM2.5 pollution as serious as in the heavily polluted roadside microenvironment. All total EOM samples showed significant (p < 0.05) dose–response effects, and their effects as olive tail moment were less than the sums of the three fractions. Aromatic fractions of EOM exhibited the greatest genotoxic potencies, but polar fractions also contributed substantially to DNA‐damaging effects. Polycyclic aromatic hydrocarbons and nitrated derivatives likely are the most important species responsible for the genotoxicity of EOM in PM2.5.
Enhanced Simplified Memory-bounded A Star (SMA*+)

In 1992, Stuart Russell briefly introduced a series of memory efficient optimal search algorithms. Among which is the Simplified Memory-bounded A Star (SMA*) algorithm, unique for its explicit memory bound. Despite progress in memory efficient A Star variants, search algorithms with explicit memory bounds are absent from progress. SMA* remains the premier memory bounded optimal search algorithm. In this paper, we present an enhanced version of SMA* (SMA*+), providing a new open list, simplified implementation, and a culling heuristic function, which improves search performance through a priori knowledge of the search space. We present benchmark and comparison results with state-of-the-art optimal search algorithms, and examine the performance characteristics of SMA*+.
Distributed Spanner Approximation

We address the fundamental network design problem of constructing approximate minimum spanners. Our contributions are for the distributed setting, providing both algorithmic and hardness results. Our main hardness result is that an ∝-approximation for the minimum directed k-spanner problem for k ≥ 5 requires Ω(n/ √ ∝ logn) rounds using deterministic algorithms or Ω( √ n/ √ ∝ logn) rounds using randomized ones, in the Congest model of distributed computing. Combined with the constant-round O(nε )-approximation algorithm in the Local model of [Barenboim, Elkin and Gavoille, 2016], as well as a polylog-round (1 + ε )-approximation algorithm in the Local model that we show here, our lower bounds for the Congest model imply a strict separation between the Local and Congest models. Notably, to the best of our knowledge, this is the first separation between these models for a local approximation problem. Similarly, a separation between the directed and undirected cases is implied. We also prove a nearly-linear lower bound for the minimum weighted k-spanner problem for k ≥ 4, and we show lower bounds for the weighted 2-spanner problem. On the algorithmic side, apart from the aforementioned (1 + ε )- approximation algorithm for minimum k-spanners, our main contribution is a new distributed construction of minimum 2-spanners that uses only polynomial local computations. Our algorithm has a guaranteed approximation ratio of O(log(m/n)) for a graph with n vertices andm edges, which matches the best known ratio for polynomial time sequential algorithms [Kortsarz and Peleg, 1994], and is tight if we restrict ourselves to polynomial local computations. Our approach allows us to extend our algorithm to work also for the directed, weighted, and client-server variants of the problem. It also provides a Congest algorithm for the minimum dominating set problem, with a guaranteed O(log Δ) approximation ratio.
Silkworm: A Promising Model Organism in Life Science

Abstract As an important economic insect, silkworm Bombyx mori (L.) (Lepidoptera: Bombycidae) has numerous advantages in life science, such as low breeding cost, large progeny size, short generation time, and clear genetic background. Additionally, there are rich genetic resources associated with silkworms. The completion of the silkworm genome has further accelerated it to be a modern model organism in life science. Genomic studies showed that some silkworm genes are highly homologous to certain genes related to human hereditary disease and, therefore, are a candidate model for studying human disease. In this article, we provided a review of silkworm as an important model in various research areas, including human disease, screening of antimicrobial agents, environmental safety monitoring, and antitumor studies. In addition, the application potentiality of silkworm model in life sciences was discussed.
Hardware Implementation of Speech Recognition Using MFCC and Euclidean Distance

This paper suggests Digital Signal processor (DSP) based speech recognition system with improved performance in terms of recognition accuracies and computational cost. The comprehensive surrey of various approaches of feature extraction like Mel filter banks with Mel Frequency Cepstrum Coefficients (MFCC). This paper describes an approach of isolated speech recognition by Digital Signal Processor TMS320C6713 using Mel scale Frequency Cepstral Coefficients and Euclidean distance. Several features are extracted from speech signal of spoken words. An experiments database of total five speakers, speaking 5-10 words each is collected under acoustically controlled room is taken. MFCC are extracted from speech signal of spoken words. To compare inter speaking differences Euclidean distance is used
Isolation and Identification of Enterococcus Faecium and Enterococcus Cecorum from Bovine Rumen Using Modern Techniques

This study aimed to isolate Enterococcus sp. from bovine rumen samples. Enterococci are the dominant bacteria in the rumen. Isolation were carried out using classical method by using Streptococcus selective medium then the isolates were identified using modern techniques by real time PCR, gel electrophoresis and DNA sequencing techniques. Results showed that Enterococcus sp. enumerated in the range from 10 to 10 CFU/mL. One of the isolates identified as Enterococcus faecium and two other isolates were Enterococcus cecorum.
Neurodevelopmental outcomes in children with HIV infection under 3 years of age

Following the introduction of combination antiretroviral therapy, children vertically infected with the human immunodeficiency virus (HIV‐1) living in the developed world are surviving into adult life. This paper reviews the neurodevelopmental outcomes of 62 consecutively‐presenting children with HIV‐1 infection diagnosed before 3 years of age (32 males, 30 females; median age at presentation 6mo). Neurological and developmental data are presented with immunological and virological responses to antiretroviral therapy. Fourteen children (22%) had abnormal neurological signs and 25 (40%) demonstrated significant developmental delay on standardized developmental assessments. Children presenting with more severe HIV‐1 disease and immune compromise had significantly more abnormal neurological signs and developmental delays than children presenting with milder HIV‐1 symptomatology. Immune function, control of HIV‐1 viral replication, and growth parameters improved with antiretroviral therapy (median age at last follow‐up 7y 3mo); however, abnormal neurological signs and significant gross motor difficulties persisted.
A survey of Parkinson's disease patients: most bothersome symptoms and coping preferences.

BACKGROUND Treatment for Parkinson's disease (PD) is symptomatic. Health professionals must therefore understand which of the many motor and non-motor problems that patients experience are the most troublesome, and what types of assistance patients believe would best help them cope with these problems. OBJECTIVE To identify and understand potential issues of importance to patients with Parkinson's Disease. METHODS We conducted surveys with 75 patients with PD in a Movement Disorders Program. We asked about: the two most bothersome PD-related problems, methods for coping with these problems, what motor and non-motor PD-related problems patients needed the most help with, and what a comprehensive assistance program for PD patients and caregivers should include. We used qualitative data analysis techniques to summarize responses. RESULTS The most bothersome problems cited were: tremors, lack of mobility, pain, imbalance, lack of energy/fatigue, having to give up previously enjoyed activities, dysarthria, and anxiety or depression. Frequently cited ways to cope with different types of problems included medications, physical activity, instrumental or practical support, and emotional support. When asked specifically about which non-motor problems elicited the most need for help, respondents most commonly mentioned depression and anxiety, "nothing," or cognitive problems. Participants suggested that a comprehensive assistance program for people with PD and their caregivers should include education, physical activity, and emotional support. CONCLUSIONS RESULTS from this survey highlight the diversity of patient experiences with PD, and the importance of strategies for coping with both motor and non-motor symptoms associated with Parkinson's Disease (in addition to medications).
Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases

Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed disparity in T2D incidence rates across ethnic populations.
Fair Value Reclassifications of Financial Assets During the Financial Crisis

This study examines whether reclassifications of financial assets out of fair value categories during a market downturn are associated with regulatory benefits and informational costs. We find that the severity of regulatory capital restrictions and the lack of prudential filters for unrealized fair value changes are positively associated with a bank’s reclassification choice. For a small group of banks that have a high reclassification likelihood and the greatest need for additional regulatory capital, we observe a positive stock market reaction around the announcement of the new accounting option. For another group of banks that were initially not expected to reclassify, we find that abnormal stock returns around the announcement of the accounting choice increase in the regulatory capital effect of the reclassification. Finally, we document a positive association between banks’ bid-ask spreads and the reclassification choice for those banks that do not provide complete IFRS 7 disclosures about the unrecognized fair value changes.
Evaluation of a Methodology for Automated Cell Counting for Streak ModeImaging Flow Cytometry

Identification of Circulating Tumor Cells (CTCs) has shown promising clinical applications, but since CTCs are found in very low concentration in blood large sample volumes are needed for meaningful enumeration. This issue impedes the analysis of CTCs using standard flow cytometry due to its low throughput. To address this issue, a high throughput microfluidic cytometer was recently developed using a wide field flow- flow cell instead of the conventional narrow hydrodynamic focusing cells (used in traditional flow cytometry) enabling analysis of large volumes at lower flow rate. This wide-field flow cytometer adopts a technique known as “streak photography” where exposure times and flow velocities are set such that the particles are imaged as short “streaks”. Since streaks are imaged with large number of pixels, they are easily distinguished from the noise which appears as “speckles” increasing the detection capabilities of the device, making it more suitable for analysis using current low sensitivity, high noise webcams or mobile phone cameras. The non-stationary nature of the high noisy background found in streak cytometry introduces additional challenges for automated cell counting methods using traditional cell detection techniques such TLC, CellProfiler, CellTracker and other tools based in traditional edge detection (e.g., Canny based filters) or manual thresholding. In order to address this issue, we developed a new automated enumeration approach that does not rely on edge detection or manual thresholding of individual cells, rather is based in image quantizing, morphological operations, 2D order-statistic filtering and decisions rules that take into account knowledge of the structure and expected location of the streaks in consecutive frames. We evaluated our approach comparing it with two current methods representing the major computational modalities for cell detection: CellTrack (based in edge detection) and MTrack2 (based in manual thresholding). Samples of 1 cell/mL nominal concentration were analyzed in batch size of 30 mL at flow rate of 10 mL/min and imaged at 4 frames per second (fps), the files were saved in uncompressed AVI format files. The cells were annotated and the signal to noise ratio (SNR) was calculated. For samples with average SNR greater than 4.4 dB, our method achieved a sensitivity of 91% compared to CellTrack (60%) and MTrack2 (71%). The True Positive Rate (TPR) of cells detected was 0.93 for our method compared with 0.80 for Mtrack2 and 0.29 for CellTrack. This demonstrated the ability of the algorithm to count rare cells with high accuracy for concentrations of 1 cell/mL with SNR greater than 4.4 dB. This cell counting capability will enable to automate low cost imaging flow cytometry based on CCD detector and the expansion of cell-based clinical diagnostics in resource-poor settings.
Overexpression of Cyclooxygenase-2 Is Sufficient to Induce Tumorigenesis in Transgenic Mice*

The cyclooxygenase (COX)-2 gene encodes an inducible prostaglandin synthase enzyme that is overexpressed in adenocarcinomas and other tumors. Deletion of the murine Cox-2 gene inMin mice reduced the incidence of intestinal tumors, suggesting that it is required for tumorigenesis. However, it is not known if overexpression of Cox-2 is sufficient to induce tumorigenic transformation. We have derived transgenic mice that overexpress the human COX-2 gene in the mammary glands using the murine mammary tumor virus promoter. The human Cox-2 mRNA and protein are expressed in mammary glands of female transgenic mice and were strongly induced during pregnancy and lactation. Female virgin Cox-2 transgenic mice showed precocious lobuloalveolar differentiation and enhanced expression of the β-casein gene, which was inhibited by the Cox inhibitor indomethacin. Mammary gland involution was delayed in Cox-2 transgenic mice with a decrease in apoptotic index of mammary epithelial cells. Multiparous but not virgin females exhibited a greatly exaggerated incidence of focal mammary gland hyperplasia, dysplasia, and transformation into metastatic tumors. Cox-2-induced tumor tissue expressed reduced levels of the proapoptotic proteins Bax and Bcl-xL and an increase in the anti-apoptotic protein Bcl-2, suggesting that decreased apoptosis of mammary epithelial cells contributes to tumorigenesis. These data indicate that enhanced Cox-2 expression is sufficient to induce mammary gland tumorigenesis. Therefore, inhibition of Cox-2 may represent a mechanism-based chemopreventive approach for carcinogenesis.