Miracle-dz/UniFAR-FTUs huggingface dataset:
Amnibacterium endophyticum sp. nov., an endophytic actinobacterium isolated from Aegiceras corniculatum.

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and short-rod-shaped actinobacterium, designated strain 1T4Z-3T, was isolated from a piece of surface-sterilized branch of Aegiceras corniculatum collected from the Cotai Ecological Zones in Macao, China. Comparative 16S rRNA gene sequence analysis showed that strain 1T4Z-3T was clearly affiliated to the genus Amnibacterium and exhibited 97.9 % gene sequence similarity to Amnibacterium kyonggiense JCM 16463T, 97.3 % gene sequence similarity to Amnibacterium soli JCM 19015T and less than 96.4 % gene sequence similarities to other genera of the family Microbacteriaceae. Strain 1T4Z-3T had L-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid. The major fatty acids (>10 % of total fatty acids) were iso-C16 : 0 (46.6 %) and anteiso-C15 : 0 (27.3 %). The predominant menaquinones of strain 1T4Z-3T were MK-11 (81.4 %) and MK-12 (14.1 %). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids, four unidentified phospholipids and two unidentified lipids. The DNA G+C content of strain 1T4Z-3T was 71.4 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain 1T4Z-3T is considered to represent a novel species of the genus Amnibacterium, for which the name Amnibacterium endophyticum sp. nov. is proposed. The type strain of Amnibacterium endophyticum is 1T4Z-3T (=KCTC 39983T=CGMCC 1.16066T).
Venous thromboembolism during pregnancy is not associated with persistent elevated activated protein C (APC) sensitivity ratio based on the endogenous thrombin potential

Summary Women who are using oral contraceptives can acquire APC resistance, measured by the effect of APC on the endogenous thrombin potential (ETP). The objective of our study was to examine whether persistentAPC resistance determined with an ETP-based normalized APC sensitivity ratio (nAPCsr) is a risk marker for venous thromboembolism in women with pregnancy-associated thromboembolism. We determined the activities of antithrombin, protein C, protein S, and performed a genetic analysis of factor V Leiden G1691A, prothrombin mutation G20210A, and methylenetetrahydrofolate reductase mutation (MTHFR C677T) in 65 women with venous thromboembolism during pregnancy or the puerperium and in 114 normal women. A significantly (p<0.05) higher nAPCsr was present in normal women using hormones, in younger women (≤ 45 yrs), and in women with carrier status of factorV Leiden. In normal women without factor V Leiden a significant (p< 0.05) negative correlation of nAPCsr with age (r= –0.39),antithrombin activity (r= –0.38),protein S activity (r= –0,26),and a significant positive correlation with hormone intake (r= 0.36) was present. nAPCsr is influenced by several coagulation parameters, which are modified by the use of oral contraceptives. Consequently, a multivariate analysis of our data did not show a significant association of nAPCsr to venous thromboembolism, neither as a continuous variable (odds ratio 0.8, 95% CI 0.6–1.1, p=0.10) nor using a cutoff value (nAPCsr cut-off 3.1: odds ratio 1.2, 95% CI 0.3–5.3, p=0.77). Our study demonstrates that nAPCsr is not a risk marker for pregnancy-associated venous thromboembolism.
Safe delivery care practices in western Nepal: Does women’s autonomy influence the utilization of skilled care at birth?

Despite various efforts to increase the utilization of skilled birth attendants (SBA), nearly two-thirds of deliveries take place at home without the assistance of SBAs in Nepal. We hypothesized that the ability of women to take decisions about their own lives—women’s autonomy—plays an important part in birth choices. To know this, we conducted a community-based cross-sectional study for assessing women’s autonomy and utilization of safe delivery care service in Kapilvastu district of Nepal from June to October 2014. We used multivariate modeling to associate socioeconomic factors and women’s autonomy with the utilization of safe delivery care services. Just over one-third of women sought institutional delivery care during the birth of their last child. Out of the total deliveries at health facilities, nearly 58% women visited health facility for self-reported emergency obstructive care. Only 6.2% home deliveries were handled by health workers and 14.7% women used the safe delivery kit for home delivery care. Higher levels of women’s education had a strong positive association (odds ratio = 24.11, CI = 9.43–61.64) with institutional delivery care. Stratified analysis showed that when the husband is educated, women’s education seems to work partly through their autonomy in decision making. Educational status of women emerged as one of the key predictors of the utilization of delivery care services in Kapilvastu district. Economic status of household and husband’s education are other dominant predictors of the utilization of safe delivery care services. Improving the economic and educational status may be the way out for improving the proportion of institutional deliveries. Women’s autonomy may be an important mediating factor in this pathway.
Taking Neighborhood Health to Heart (TNH2H): Building a Community-Based Participatory Data System

Background Healthy People 2020 calls for increased monitoring of local health and health disparities, but successful models of designing and implementing data collection systems for this purpose are lacking. Community Context We describe the process, methods, and outcomes of a community-based participatory research initiative, Taking Neighborhood Health to Heart, designed to collect and disseminate comprehensive health data from 5 diverse urban neighborhoods in Denver, Colorado. Methods Since its beginning in 2006, this initiative has involved community members in collection of individual health surveys from 1,146 households; audits of sidewalks, buildings, and other built environment features in 412 neighborhood blocks; audits of availability, price, and quality of fresh produce in 69 local stores; and audits of conditions and amenities in 20 local parks. Community members and researchers share, interpret, and disseminate these data through a joint data review and dissemination committee. Outcome Through our community-based data collection system, Taking Neighborhood Health to Heart has been able to collect, analyze, and disseminate locally relevant data on people and neighborhoods to monitor heath and health disparities. Interpretation Since 2006, the initiative has sustained its focus on community-based participatory research that targets collection and dissemination of local health data. We have used this information to identify salient health issues and advocate for neighborhood programs, policies, and environmental changes to built and social features of neighborhoods that have historically led to unequal opportunities and social disadvantage.
Investor Concentration, Flows, and Cash Holdings: Evidence from Hedge Funds

We show that when only a few investors own a substantial portion of a hedge fund's net asset value, flow volatility increases because investors' exogenous, idiosyncratic liquidity shocks are not diversified away. Using confidential regulatory filings, we confirm that high investor concentration hedge funds experience more volatile flows. These hedge funds hold more cash and liquid assets, which help absorb large, unexpected outflows. Such funds have to pay a liquidity premium and generate lower risk-adjusted returns. Investor concentration does not affect flow-performance sensitivity. These results are robust to including lock-up and redemption periods, strategy, manager ownership, and other controls.
The impact of combined interpretation of localization studies on image-guided surgical approaches for primary hyperparathyroidism.

BACKGROUND The impact of single and combined interpretations of ultrasonography and sestamibi scintigraphy to select the appropriate surgical approach in patients with primary hyperparathyroidism were evaluated retrospectively. METHODS A total of 183 patients with primary hyperparathyroidism who were evaluated preoperatively using both ultrasonography and sestamibi scintigraphy were included in the study. The results of preoperative localization studies were correlated with intraoperative findings and postoperative histopathological results. The localization rates of individual and combined interpretations of ultrasonography and sestamibi scintigraphy were evaluated. RESULTS The overall sensitivity and the positive predictive value of ultrasonography and sestamibi scintigraphy were 76% and 90%, and 81% and 91%, respectively. Both imaging studies were concordant for the same localization(s) in 121 (66%) of 183 patients. The prevalence rates of single-gland and multiglandular disease were 90% (N.=109) and 10% (N.=12), respectively, in patients with concordant results (P=0.0001). The overall rate of localization was 91% (N.=110) in these patients. In these patients with concordant results, the sensitivity and the positive predictive value of imaging were 91% and 100%, respectively. The localization rates were 96% and 42% for single-gland and multiglandular disease, respectively (P=0.0001). Of the remaining 62 patients, 50 had negative imaging with either ultrasonography (N.=29) or MIBI (N.=21). Of the 29 patients with negative ultrasonography results, sestamibi scintigraphy was positive in 23. Of the 21 patients with negative sestamibi scintigraphy imaging, ultrasonography was positive in 15. Thus, 38 patients had a single positive imaging result. The majority (95%) of these 38 patients had single-gland disease, and the rate of multiglandular disease was 5% (P=0.0001). The rate of localization was 95% (36/38) in patients with a single positive imaging study. Eighteen patients had discordant imaging results. CONCLUSIONS The overall rate of localization in primary hyperparathyroidism is greater than 90% if ultrasonography and sestamibi scintigraphy are concordantly positive for the same localization, and the prevalence of multiglandular disease is low in patients with concordant imaging. An image-guided surgical approach and selective parathyroidectomy exhibit high cure rates in the setting of concordantly positive sestamibi and ultrasonography results, even if intraoperative parathormone monitoring is not used.
Concordant optimal molecular and cytogenetic responses at both 3 and 6 months predict a higher probability of MR4.5 achievement in patients with chronic myeloid leukemia treated with imatinib

Abstract To investigate the impact of the combination of early molecular and cytogenetic responses on the achievement of MR4.5, 228 newly diagnosed chronic phase chronic myeloid leukemia patients treated with imatinib were categorized into 3-month and 6-month concordant optimal, discordant, concordant warning, and failure groups. Among them, 85.3% at 3 months and 78.1% at 6 months had concordant molecularly and cytogenetically defined responses. At both 3 and 6 months, patients with discordant, concordant warning and failure responses had similar 3-year MR4.5 rates, and all were significantly lower than the rate in patients with concordant optimal responses. Patients with concurrent 3-month and 6-month concordant optimal responses had a significantly higher 3-year MR4.5 rate than those with other responses, and 3-month and 6-month concurrent molecular optimal, but not cytogenetic optimal responses. Therefore, achieving concordant optimal molecular and cytogenetic responses at both 3 and 6 months with imatinib treatment are associated with MR4.5 achievement.
Large-Scale Climate Effects Meet an Amazonian Butterfly: Which Population Parameters Respond to El Niño?

Abstract One of the most tangible outcomes of climate change is change in the frequency of El Niño/La Niña events. They have a large impact on rainfall in the Western hemisphere, but their impact on tropical fauna is largely unknown. A decade long capture-mark-recapture study of the widespread Ecuadorian butterfly Nessaea hewitsoni (Felder & Felder) from an intact forest allowed us to analyze patterns of monthly and seasonal population dynamics before, during, and after an El Niño event. El Niño events did not affect long-term population size, but a 5-month delayed El Niño led to temporary emigration of females, with their subsequent return. Increased rainfall correlated with reduced survival in both sexes, but this effect was twice as strong in females. This investigation is the longest, continuous population study on any Neotropical insect species. Though we sampled on a modest scale, the magnitude of El Niño events suggests that our findings likely reflect insect population responses across a much larger portion of Amazonian forests.This study underscores the importance of analyzing multiple, interacting population parameters beyond local abundance in order to understand the biotic responses to El Niño and climate change in tropical systems. Had our analyses not included temporary emigration, no effect would have been detected because El Niño did not affect local population abundance.
URBAN VEGETATION DETECTION USING HIGH DENSITY FULL-WAVEFORM AIRBORNE LIDAR DATA-COMBINATION OF OBJECT-BASED IMAGE AND POINT CLOUD ANALYSIS

In this paper, a new GIS workflow for fully automated urban vegetation and tree parameter extraction from airborne LiDAR data is presented. The strengths of both rasterand point cloud-based methods are combined, in order to derive a vegetation map layer as well as single tree parameters (e.g. tree height and crown width) in an efficient way. The workflow is implemented in GRASS GIS making use of standard GIS functionality and newly developed tools providing access to point cloud analysis. An edge-based segmentation delineates potential tree crowns, which are further aggregated to single trees or group of trees by using local topological information (e.g. percentage of outline touched by neighbors) and constraints on segment geometry (e.g. shape of segments). Furthermore, the classification makes use of segment attributes that have been extracted from the full-waveform point cloud (e.g. percentage of first echoes, echo width and signal amplitude). A representative study area in the City of Vienna is used to demonstrate the applicability of the developed object-based GIS workflow. Buildings and vegetation objects could be separated with high accuracy, where at maximum 14% of classified vegetation segments confuse with buildings (mainly building edges). Concluding, the unique high density (50 pts/m) full-waveform LiDAR data open a new scale in 3D object extraction but demanding for novel strategies in object-based raster and point cloud analysis. * Corresponding author.
Metabolomic Characterization of Hepatocellular Carcinoma in Patients with Liver Cirrhosis for Biomarker Discovery

Background: Metabolomics plays an important role in providing insight into the etiology and mechanisms of hepatocellular carcinoma (HCC). This is accomplished by a comprehensive analysis of patterns involved in metabolic alterations in human specimens. This study compares the levels of plasma metabolites in HCC cases versus cirrhotic patients and evaluates the ability of candidate metabolites in distinguishing the two groups. Also, it investigates the combined use of metabolites and clinical covariates for detection of HCC in patients with liver cirrhosis. Methods: Untargeted analysis of metabolites in plasma from 128 subjects (63 HCC cases and 65 cirrhotic controls) was conducted using gas chromatography coupled to mass spectrometry (GC-MS). This was followed by targeted evaluation of selected metabolites. LASSO regression was used to select a set of metabolites and clinical covariates that are associated with HCC. The performance of candidate biomarkers in distinguishing HCC from cirrhosis was evaluated through a leave-one-out cross-validation based on area under the receiver operating characteristics (ROC) curve. Results: We identified 11 metabolites and three clinical covariates that differentiated HCC cases from cirrhotic controls. Combining these features in a panel for disease classification using support vector machines (SVM) yielded better area under the ROC curve compared with alpha-fetoprotein (AFP). Conclusions: This study demonstrates the combination of metabolites and clinical covariates as an effective approach for early detection of HCC in patients with liver cirrhosis. Impact: Further investigation of these findings may improve understanding of HCC pathophysiology and possible implication of the metabolites in HCC prevention and diagnosis. Cancer Epidemiol Biomarkers Prev; 26(5); 675–83. ©2016 AACR.
Enzymatic Preparation of 2,5-Furandicarboxylic Acid (FDCA)—A Substitute of Terephthalic Acid—By the Joined Action of Three Fungal Enzymes

Enzymatic oxidation of 5-hydroxymethylfurfural (HMF) and its oxidized derivatives was studied using three fungal enzymes: wild-type aryl alcohol oxidase (AAO) from three fungal species, wild-type peroxygenase from Agrocybe aegerita (AaeUPO), and recombinant galactose oxidase (GAO). The effect of pH on different reaction steps was evaluated and apparent kinetic data (Michaelis-Menten constants, turnover numbers, specific constants) were calculated for different enzyme-substrate ratios and enzyme combinations. Finally, the target product, 2,5-furandicarboxylic acid (FDCA), was prepared in a multi-enzyme cascade reaction combining three fungal oxidoreductases at micro-scale. Furthermore, an oxidase-like reaction is proposed for heme-containing peroxidases, such as UPO, horseradish peroxidase, or catalase, causing the conversion of 5-formyl-2-furancarboxylic acid into FDCA in the absence of exogenous hydrogen peroxide.
Developing a Baccalaureate Digital Forensics Major

As colleges and universities consider instituting a bachelor’s degree in digital forensics or computer forensics, there are numerous questions to be addressed. While some of these normally occur in the development of any new major, there are aspects of digital forensics which do not often (if ever) occur in other majors. We discuss the issues that should be resolved in the development of a baccalaureate degree program in digital forensics.
4 Complex genetic models

The map of our chromosomes produced by the Human Genome Project has documented similarities and differences between individuals and has shown that people share approximately the same DNA with the exception of about 0.1% nucleotide bases [452]. These variations are called single nucleotide polymorphisms (SNPs) and occur when a single nucleotide (A, T, C, or G) in the genome sequence is altered. Some of these variants may be the cause of ‘monogenic diseases’ in which a single gene is responsible for causing the disease. This happens when the gene is defective so that a mutation of the DNA sequence of the gene determines a change in the associated protein. Our cells contain two copies of each chromosome and monogenic diseases are classified as ‘dominant’ or ‘recessive’ based on the number of copies of the mutated variants that are necessary for the disease to manifest. A dominant disease needs only one mutated variant to manifest while a recessive disease needs two mutated variants to manifest and one mutated variant makes a subject only a carrier of the disease. A carrier can transmit the mutated variant to the offspring, but not the disease and a recessive disease can only be
Comparison of human gastrocnemius forces predicted by Hill-type muscle models and estimated from ultrasound images

ABSTRACT Hill-type models are ubiquitous in the field of biomechanics, providing estimates of a muscle's force as a function of its activation state and its assumed force–length and force–velocity properties. However, despite their routine use, the accuracy with which Hill-type models predict the forces generated by muscles during submaximal, dynamic tasks remains largely unknown. This study compared human gastrocnemius forces predicted by Hill-type models with the forces estimated from ultrasound-based measures of tendon length changes and stiffness during cycling, over a range of loads and cadences. We tested both a traditional model, with one contractile element, and a differential model, with two contractile elements that accounted for independent contributions of slow and fast muscle fibres. Both models were driven by subject-specific, ultrasound-based measures of fascicle lengths, velocities and pennation angles and by activation patterns of slow and fast muscle fibres derived from surface electromyographic recordings. The models predicted, on average, 54% of the time-varying gastrocnemius forces estimated from the ultrasound-based methods. However, differences between predicted and estimated forces were smaller under low speed–high activation conditions, with models able to predict nearly 80% of the gastrocnemius force over a complete pedal cycle. Additionally, the predictions from the Hill-type muscle models tested here showed that a similar pattern of force production could be achieved for most conditions with and without accounting for the independent contributions of different muscle fibre types. Summary: Hill-type muscle models, driven by EMG and ultrasound-based measures of fascicle behaviour, predict 40–80% of gastrocnemius forces, as confirmed via ultrasound-based estimates of tendon strains.
Brain dopamine and serotonin transporter binding are associated with visual attention bias for food in lean men

Background In rodents, the striatal dopamine (DA) system and the (hypo)thalamic serotonin (5-HT) system are involved in the regulation of feeding behavior. In lean humans, little is known about the relationship between these brain neurotransmitter systems and feeding. We studied the relationship between striatal DA transporters (DAT) and diencephalic 5-HT transporters (SERT), behavioral tasks and questionnaires, and food intake. Method We measured striatal DAT and diencephalic SERT binding with [123I]FP-CIT SPECT in 36 lean male subjects. Visual attention bias for food (detection speed and distraction time) and degree of impulsivity were measured using response-latency-based computer tasks. Craving and emotional eating were assessed with questionnaires and ratings of hunger by means of VAS scores. Food intake was assessed through a self-reported online diet journal. Results Striatal DAT and diencephalic SERT binding negatively correlated with food detection speed (p = 0.008, r = −0.50 and p = 0.002, r = −0.57, respectively), but not with food distraction time, ratings of hunger, craving or impulsivity. Striatal DAT and diencephalic SERT binding did not correlate with free choice food intake, whereas food detection speed positively correlated with total caloric intake (p = 0.001, r = 0.60), protein intake (p = 0.01, r = 0.44), carbohydrate intake (p = 0.03, r = 0.39) and fat intake (p = 0.06, r = 0.35). Conclusions These results indicate a role for the central 5-HT and DA system in the regulation of visual attention bias for food, which contributes to the motivation to eat, in non-obese, healthy humans. In addition, this study confirms that food detection speed, measured with the latency-based computer task, positively correlates with total food and macronutrient intake.