Miracle-dz/UniFAR-FTUs huggingface dataset:
Heart Rate Variability: Measurement and Clinical Utility

Electrocardiographic RR intervals fluctuate cyclically, modulated by ventilation, baroreflexes, and other genetic and environmental factors that are mediated through the autonomic nervous system. Short term electrocardiographic recordings (5 to 15 minutes), made under controlled conditions, e.g., lying supine or standing or tilted upright can elucidate physiologic, pharmacologic, or pathologic changes in autonomic nervous system function. Long‐term, usually 24‐hour recordings, can be used to assess autonomic nervous responses during normal daily activities in health, disease, and in response to therapeutic interventions, e.g., exercise or drugs. RR interval variability is useful for assessing risk of cardiovascular death or arrhythmic events, especially when combined with other tests, e.g., left ventricular ejection fraction or ventricular arrhythmias.
Sorting specimen‐rich invertebrate samples with cost‐effective NGS barcodes: Validating a reverse workflow for specimen processing

Biologists frequently sort specimen‐rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a “reverse workflow” is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next‐generation sequencing (NGS) barcoding pipeline that allows for cost‐effective high‐throughput generation of short specimen‐specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next‐generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88–90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.
Improving Performance of GMR Sensors

Giant magnetoresistance (GMR) sensors are assumed as an important role in magnetic field sensing applications because of their small size, high sensitivity, large frequency response, low power consumption, and relatively low cost. In all these applications, it is very important to estimate and possibly reduce the measurement uncertainty related to the use of these sensors. In this paper, the metrological characterization of GMR magnetometers highlights the contributions to measurement uncertainty of hysteresis, nonlinearity, and operating temperature. Starting from this knowledge, an automatic procedure for calibration and adjustment of GMR magnetometers is setup. This procedure, based on a mixed hardware-software solution, allows a meaningful reduction of the measurement uncertainty for both ac and dc magnetic field amplitude measurements using GMRs.
RETAIL FOOD PRICE FORECASTING AT ERS: THE PROCESS, METHODOLOGY, AND PERFORMANCE FROM 1984 TO 1997

Forecasting retail food prices has become increasingly important to the U.S. Department of Agriculture (USDA). This is due to the changing structure of food and agricultural economies and the important signals the forecasts provide to farmers, processors, wholesalers, consumers, and policymakers. The American food system is going through fundamental structural changes. It is unclear how these changes will affect the cyclical variation of food price markups and translate into changes in retail food prices. The only government entity that systematically examines food prices and provides food price forecasts (on an annual basis) is the Economic Research Service, and agency of USDA. This report explains the ERS procedures in forecasting food prices and assesses how changes in the current procedures would improve the quality of the forecasts.
Histone H3 Lysine 36 Methylation Targets the Isw1b Remodeling Complex to Chromatin

ABSTRACT Histone H3 lysine 36 methylation is a ubiquitous hallmark of productive transcription elongation. Despite the prevalence of this histone posttranslational modification, however, the downstream functions triggered by this mark are not well understood. In this study, we showed that H3K36 methylation promoted the chromatin interaction of the Isw1b chromatin-remodeling complex in Saccharomyces cerevisiae. Similar to H3K36 methylation, Isw1b was found at the mid- and 3′ regions of transcribed genes genome wide, and its presence at active genes was dependent on H3K36 methylation and the PWWP domain of the Isw1b subunit, Ioc4. Moreover, purified Isw1b preferentially interacted with recombinant nucleosomes that were methylated at lysine 36, and this interaction also required the Ioc4 PWWP domain. While H3K36 methylation has been shown to regulate the binding of numerous factors, this is the first time that it has been shown to facilitate targeting of a chromatin-remodeling complex.
The influence of body mass index on growth hormone secretion in normal and short statured children.

Obesity is one of the factors which limits the value of growth hormone (GH) provocation tests in the diagnosis of GH deficiency. We have therefore examined (1) the relationship between urinary GH (uGH), a physiological parameter of GH secretion, and percent ideal body mass index (BMI%), an indirect estimate of body fat, in 528 schoolchildren; and (2) the extent to which peak arginine stimulated (0.5 g/kg i.v.) GH concentrations were influenced by BMI% in 176 short normal (SN) children and 48 girls with Turner syndrome (TS). The mean BMI% (SD) for each group was 102.9 (10.8) in schoolboys, 102.7 (13.4) in schoolgirls, 95.8 (13.9) in SN boys, 98.2 (21.4) in SN girls and 105.9 (18.0) in TS. BMI% correlated inversely with log uGH in school-children (boys r = -0.16, P = 0.01; girls r = -0.25, P < 0.001). However, if each sex was subdivided by pubertal status, the inverse relationship only persisted in pubertal (boys r = -0.18, P = 0.04; girls r = -0.39, P < 0.001) but not prepubertal children (boys r = -0.1, P = 0.3; girls r = -0.11, P = 0.3). BMI% was also inversely related to log peak stimulated GH concentration in SN girls (r = -0.49, P < 0.001) but not SN boys (r = -0.14, P = 0.2) or girls with TS (r = 0.19, P = 0.2). The inverse relationship between normal body fat and physiological GH secretion becomes significant during puberty; in girls it accounts for 15% of the variability in uGH excretion. (ABSTRACT TRUNCATED AT 250 WORDS)
Temperature variability is integrated by a spatially embedded decision-making center to break dormancy in Arabidopsis seeds

Significance Both plants and animals make decisions in response to the environment to maximize their fitness. Plants use dormancy in seeds to move through time and space, and timing of the transition to germination is influenced by external cues, including temperature. Here, we report the presence of a decision-making center within the root tip of dormant seeds and demonstrate that it shares a similar configuration as some systems within the human brain. Unlike in humans, where this spatial structure is used to filter out noisy inputs from the environment, seeds use this arrangement to harness fluctuating temperatures and stimulate the termination of dormancy. Variable inputs therefore act as an instructive signal for seeds, enhancing the accuracy with which plants are established in ecosystems. Plants perceive and integrate information from the environment to time critical transitions in their life cycle. Some mechanisms underlying this quantitative signal processing have been described, whereas others await discovery. Seeds have evolved a mechanism to integrate environmental information by regulating the abundance of the antagonistically acting hormones abscisic acid (ABA) and gibberellin (GA). Here, we show that hormone metabolic interactions and their feedbacks are sufficient to create a bistable developmental fate switch in Arabidopsis seeds. A digital single-cell atlas mapping the distribution of hormone metabolic and response components revealed their enrichment within the embryonic radicle, identifying the presence of a decision-making center within dormant seeds. The responses to both GA and ABA were found to occur within distinct cell types, suggesting cross-talk occurs at the level of hormone transport between these signaling centers. We describe theoretically, and demonstrate experimentally, that this spatial separation within the decision-making center is required to process variable temperature inputs from the environment to promote the breaking of dormancy. In contrast to other noise-filtering systems, including human neurons, the functional role of this spatial embedding is to leverage variability in temperature to transduce a fate-switching signal within this biological system. Fluctuating inputs therefore act as an instructive signal for seeds, enhancing the accuracy with which plants are established in ecosystems, and distributed computation within the radicle underlies this signal integration mechanism.
Proteome analysis in the study of the bacterial heat-shock response.

In recent years, it has become clear that, in addition to the regulation of the expression of specific genes, there are global regulatory systems that control the simultaneous expression of a large number of genes in response to a variety of environmental stresses. The first of these global control systems, and of substantial importance, is the heat-shock response. The heat-shock response is characterized by the induction of a large set of proteins (heat-shock proteins-HSPs) upon shifts to higher temperature and upon exposure to conditions in which proteins are denatured (i.e., alcohols, heavy metals). The heat-shock response is universal and many of the heat-shock proteins are highly conserved among species. In bacteria, the heat-shock response has been studied extensively in several Gram-positive bacteria (Bacillus subtilis) and in the Gram-negative bacteria (i.e., Escherichia coli, Agrobacterium tumefaciens). The first recognition of the molecular abundance of the bacterial heat-shock proteins took place with the introduction of high-resolution two-dimensional polyacrylamide gels (2D gels) to analyze complex mixtures of cellular proteins. Two-dimensional gels, followed by mass spectrometry, were used to define the heat-shock stimulons in several bacteria, and to study the regulatory elements that control the heat-shock response. Here, we review the heat-shock response and its regulation in bacteria. The review will emphasize the use of proteome analysis in the study of this response, and will point out those open questions that can be investigated with proteomics, including mass spectrometry techniques.
Long‐term survival with low toxicity after allogeneic transplantation for acute myeloid leukaemia and myelodysplasia using non‐myeloablative conditioning without T cell depletion

The toxicity burden and long‐term anti‐leukaemic effect of non‐myeloablative (NMA) allogeneic haematopoietic stem‐cell transplantation (AHSCT) for acute myeloid leukaemia (AML) and myelodysplasia (MDS) remains undefined. We report the outcome of 56 patients with AML/MDS transplanted from human leucocyte antigen‐matched donors using NMA conditioning without T‐cell depletion. With a median follow‐up of 5 years, treatment‐related mortality was 9% and current disease‐free survival (CDFS) was 45% (overall) and 55% (patients transplanted in remission). Development of graft‐versus‐host disease upon withdrawal of post‐transplant immunosuppression was associated with less relapse and better CDFS. These data confirm that NMA AHSCT without T‐cell depletion is safe and can result in sustained remissions of AML/MDS.
Differential Cell Line Susceptibility to the Emerging Novel Human Betacoronavirus 2c EMC/2012: Implications for Disease Pathogenesis and Clinical Manifestation

Abstract The emerging novel human betacoronavirus 2c EMC/2012 (HCoV-EMC) was recently isolated from patients with severe pneumonia and renal failure and was associated with an unexplained high crude fatality rate of 56%. We performed a cell line susceptibility study with 28 cell lines. HCoV-EMC was found to infect the human respiratory tract (polarized airway epithelium cell line Calu-3, embryonic fibroblast cell line HFL, and lung adenocarcinoma cell line A549), kidney (embryonic kidney cell line HEK), intestinal tract (colorectal adenocarcinoma cell line Caco-2), liver cells (hepatocellular carcinoma cell line Huh-7), and histiocytes (malignant histiocytoma cell line His-1), as evident by detection of high or increasing viral load in culture supernatants, detection of viral nucleoprotein expression by immunostaining, and/or detection of cytopathic effects. Although an infected human neuronal cell line (NT2) and infected monocyte and T lymphocyte cell lines (THP-1, U937, and H9) had increased viral loads, their relatively lower viral production corroborated with absent nucleoprotein expression and cytopathic effects. This range of human tissue tropism is broader than that for all other HCoVs, including SARS coronavirus, HCoV-OC43, HCoV-HKU1, HCoV-229E, and HCoV-NL63, which may explain the high mortality associated with this disease. A recent cell line susceptibility study showed that HCoV-EMC can infect primate, porcine, and bat cells and therefore may jump interspecies barriers. We found that HCoV-EMC can also infect civet lung fibroblast and rabbit kidney cell lines. These findings have important implications for the diagnosis, pathogenesis, and transmission of HCoV-EMC.
Baldrige educational quality criteria as another model for accreditation in American community colleges

approved: This is a study of how the use of Baldrige Educational Quality Criteria provides community college leaders and external evaluators with richer, more meaningful data for organizational improvement, more comprehensive information about the institution, and a better means for illustrating clear connections between campus systems and processes. This study was guided by the following research questions: How do community college leaders who use Baldrige Educational Quality Criteria address institutional planning and measurements of success based on the level of value and practice of quality principles at their institution? What are the benefits and challenges for community colleges using the Baldrige Educational Quality Criteria? The study's participants included a nationwide sample of 202 community college leaders who are currently using quality principles and processes on their campuses. A total of 106 respondents or 52.5% returned the questionnaire. The study's web-based Baldrige/Institutional Effectiveness Questionnaire comprised 50 quantitative questions on a dual scale of Value and Practice; six qualitative, openended questions; and ten demographic questions. The overall findings indicated that community college leaders highly value quality principles with slightly lower corresponding scores for the equivalent practice categories. The open-ended questions yielded overwhelmingly positive testimonials from leaders regarding the strength of the Criteria for quality assurance as compared to traditional accreditation practices and models. The vast majority of responding community college leaders considered the Baldrige Educational Quality Criteria as a viable option for accreditation, but they also clearly described the challenges of meeting and applying the Criteria. The researcher concluded that the use of the Baldrige Criteria by some community colleges for accreditation might better serve the needs of these particular colleges. By incorporating Baldrige's greatest assets such as the emphasis on data gathering/data driven decision-making, the focus on the interconnectedness of all campus systems and processes, and the necessity to align the planning processes with the campus research office into the institutional accreditation process, most community colleges will realize more continuous organizational improvement. ©Copyright by Jane B. Faulkner April 30, 2002 All Rights Reserved Baldrige Educational Quality Criteria as Another Model for Accreditation in American Community Colleges
ASPsiRNA: A Resource of ASP-siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy

Allele-specific siRNAs (ASP-siRNAs) have emerged as promising therapeutic molecules owing to their selectivity to inhibit the mutant allele or associated single-nucleotide polymorphisms (SNPs) sparing the expression of the wild-type counterpart. Thus, a dedicated bioinformatics platform encompassing updated ASP-siRNAs and an algorithm for the prediction of their inhibitory efficacy will be helpful in tackling currently intractable genetic disorders. In the present study, we have developed the ASPsiRNA resource (http://crdd.osdd.net/servers/aspsirna/) covering three components viz (i) ASPsiDb, (ii) ASPsiPred, and (iii) analysis tools like ASP-siOffTar. ASPsiDb is a manually curated database harboring 4543 (including 422 chemically modified) ASP-siRNAs targeting 78 unique genes involved in 51 different diseases. It furnishes comprehensive information from experimental studies on ASP-siRNAs along with multidimensional genetic and clinical information for numerous mutations. ASPsiPred is a two-layered algorithm to predict efficacy of ASP-siRNAs for fully complementary mutant (Effmut) and wild-type allele (Effwild) with one mismatch by ASPsiPredSVM and ASPsiPredmatrix, respectively. In ASPsiPredSVM, 922 unique ASP-siRNAs with experimentally validated quantitative Effmut were used. During 10-fold cross-validation (10nCV) employing various sequence features on the training/testing dataset (T737), the best predictive model achieved a maximum Pearson’s correlation coefficient (PCC) of 0.71. Further, the accuracy of the classifier to predict Effmut against novel genes was assessed by leave one target out cross-validation approach (LOTOCV). ASPsiPredmatrix was constructed from rule-based studies describing the effect of single siRNA:mRNA mismatches on the efficacy at 19 different locations of siRNA. Thus, ASPsiRNA encompasses the first database, prediction algorithm, and off-target analysis tool that is expected to accelerate research in the field of RNAi-based therapeutics for human genetic diseases.
The Impact of Agricultural Extension Services: The Case of Grape Production in Argentina

In this paper we evaluate the impact of the provision of agricultural extension services to grape producers in Mendoza, Argentina, on yield and grape quality. Using fixed effects and matching techniques, we show that despite non-significant average treatment effects on yield, the program has large positive effects on productivity for producers who were in the bottom of the productivity distribution before launching of the program. There is also evidence of increased quality of their grapes, especially for large producers and those in the middle of the yield distribution ex-ante. However, large groups of producers did not see impact on yields or quality. Consistent with a previous qualitative evaluation of the program, these results point to the need to balance flexibility of the program with effective targeting mechanisms. Producers with different characteristics, such as land size, productivity or structure of production seek different objectives and have different needs, so that targeting these types of programs effectively to the different needs of producers would increase their effectiveness.
Complete mitochondrial genome of the golden-crowned sifaka, Propithecus tattersalli (Primates: Indriidae)

Abstract The golden-crowned sifaka, Propithecus tattersalli, is a critically endangered social lemur species that inhabits the restricted and highly fragmented semi-evergreen forests. In this study, we determined the complete mitochondrial genome sequence of this species for the first time. The results shows that this mtDNA genome is 17 099 bp in size, and comprises 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes, and one control region (D-loop). The overall base composition in descending order is A (32.91%), C (27.07%), T (27.04%), and G (12.98%), so the percentage of A and T (59.95%) is slightly higher than that of G and C. The gene order and the composition of P. tattersalli mitochondrial genome are exactly similar to those of most other vertebrates. All the genes are encoded on the heavy strand with the exception of NADH dehydrogenase subunit six (ND6) and eight tRNA genes. Phylogenetic analysis suggests that the P. tattersalli exhibits most close relationship with P. coquereli. The complete mitochondrial genome sequence presented here will be useful for further phylogenetic analysis and conservation genetic studies in P. tattersalli.
Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense

ABSTRACT Rapidly growing mycobacteria are rarely found in central nervous system infections. We describe a case of polymicrobial infection in a brain abscess including two rapidly growing Mycobacterium species, M. immunogenum and M. llatzerense. The Mycobacterium isolates were distinguishable by molecular methods, and whole-genome sequencing showed <60% pairwise nucleotide identity.
Revisiting Crisis Maps with Geo-temporal Tag Visualization

Crowd sourced crisis mapping is a relatively new phenomenon and platform that enables the collection and visualization of real-time crisis data submitted by users through social media tools and cellular technologies. Crisis maps are generally used by both state and non-state actors for sense-making and as a reference point for action. The current crisis map visualizations only show the location from which documents such as reports or short messages have been generated. Such a limited representation fails to immediately show important content, such as themes from a document and their changes over time. As a result, sense-making becomes time-consuming and cognitively demanding. We present a new visualization approach, Geo-Temporal Tag Visualization (GTViz), which treats the tags on the crowd sourced reports as spatio-temporal textual datasets. GTViz embeds a map to represent the spatial properties of the dataset and compactly shows the changes of key terms from the data source over time. We demonstrate the value of GTViz through two case studies and a controlled user study.
Error analysis and believable bound selection of line loss comparison in the distribution grid

The line loss control project is important task for energy conservation and loss reduction. The loss comparison of special lines in the distribution grid is an important part of this project. In this paper, the errors in the line loss comparison work are analyzed in detail based upon the actual working experience. A new method of believable bound selection for special line loss comparison work is introduced, and the example shows the accuracy of the method.