Miracle-dz/UniFAR-FTUs huggingface dataset:
Woody vegetation dynamics in the tropical and subtropical Andes from 2001 to 2014: Satellite image interpretation and expert validation

The interactions between climate and land‐use change are dictating the distribution of flora and fauna and reshuffling biotic community composition around the world. Tropical mountains are particularly sensitive because they often have a high human population density, a long history of agriculture, range‐restricted species, and high‐beta diversity due to a steep elevation gradient. Here we evaluated the change in distribution of woody vegetation in the tropical Andes of South America for the period 2001–2014. For the analyses we created annual land‐cover/land‐use maps using MODIS satellite data at 250 m pixel resolution, calculated the cover of woody vegetation (trees and shrubs) in 9,274 hexagons of 115.47 km2, and then determined if there was a statistically significant (p < 0.05) 14 year linear trend (positive—forest gain, negative—forest loss) within each hexagon. Of the 1,308 hexagons with significant trends, 36.6% (n = 479) lost forests and 63.4% (n = 829) gained forests. We estimated an overall net gain of ~500,000 ha in woody vegetation. Forest loss dominated the 1,000–1,499 m elevation zone and forest gain dominated above 1,500 m. The most important transitions were forest loss at lower elevations for pastures and croplands, forest gain in abandoned pastures and cropland in mid‐elevation areas, and shrub encroachment into highland grasslands. Expert validation confirmed the observed trends, but some areas of apparent forest gain were associated with new shade coffee, pine, or eucalypt plantations. In addition, after controlling for elevation and country, forest gain was associated with a decline in the rural population. Although we document an overall gain in forest cover, the recent reversal of forest gains in Colombia demonstrates that these coupled natural‐human systems are highly dynamic and there is an urgent need of a regional real‐time land‐use, biodiversity, and ecosystem services monitoring network.
Metabolic Syndrome and Cognitive Impairment among High Socioeconomic, Nondemented Older US Adults

Nondemented cognitive impairment (CI) presents opportunities for early interventions among individuals at risk for dementia. Identification of modifiable determinants is paramount to the development of effective clinical interventions. Metabolic syndrome (MetS) was theorized as a risk factor, but current research yields inconsistent findings. Few studies have examined the association between MetS and CI among US populations, and global results may be ungeneralizable. We investigated the MetS‐CI association among high socioeconomic, nondemented older US adults, examining the roles of sociodemographic, clinical, behavioral, and genetic factors.
Comparative outcomes of subcutaneous and transvenous cardioverter-defibrillators

Background: The comparative outcomes of subcutaneous implantable cardioverter-defibrillator (S-ICD) and transvenous ICD (T-ICD) have not been well studied. The aim of this study was to evaluate the safety and efficacy of currently available S-ICD and T-ICD. Methods: The study included 86 patients who received an S-ICD and 1:1 matched to those who received single-chamber T-ICD by gender, age, diagnosis, left ventricular ejection fraction (LVEF), and implant year. The clinical outcomes and implant complications were compared between the two groups. Results: The mean age of the 172 patients was 45 years, and 129 (75%) were male. The most common cardiac condition was hypertrophic cardiomyopathy (HCM, 37.8%). The mean LVEF was 50%. At a mean follow-up of 23 months, the appropriate and inappropriate ICD therapy rate were 1.2% vs. 4.7% (&khgr;2 = 1.854, P = 0.368) and 9.3% vs. 3.5% (&khgr;2 = 2.428, P = 0.211) in S-ICD and T-ICD groups respectively. There were no significant differences in device-related major and minor complications between the two groups (7.0% vs. 3.5%, &khgr;2 = 1.055, P = 0.496). The S-ICD group had higher T-wave oversensing than T-ICD group (9.3% vs. 0%, &khgr;2 = 8.390, P = 0.007). Sixty-five patients had HCM (32 in S-ICD and 33 in T-ICD). The incidence of major complications was not significantly different between the two groups. Conclusions: The efficacy of an S-ICD is comparable to that of T-ICD, especially in a dominantly HCM patient population. The S-ICD is associated with fewer major complications demanding reoperation.
The Brazilian experience of implementing the active pharmacovigilance of dolutegravir

Abstract In 2017, the Ministry of Health Brazilian started using dolutegravir (DTG) 50 mg to all people living with HIV who began antiretroviral therapy (ART) or rescue regimens. Although DTG is thought to have better tolerability levels and a lower possibility of causing adverse reactions, it is necessary to continuously evaluate the safety profile of the drug in the population. Therefore, an active pharmacovigilance project for DTG was implemented. The objective of this study was to describe the Brazilian experience of implementing pharmacovigilance and the results obtained during the period between April and December 2017. Active pharmacovigilance was implemented through patient interviews and an online questionnaire developed in the Medication Logistics Control System (SICLOM). Of the total number of people on DTG in Brazil (79,742) 90.33% participated in the project, and 2.24% of those who participated reported adverse reactions to the drug; of those who reported adverse reactions, 73.86% were on first-line ART regimens, and 26.13% were on third-line regimens. The mean age of the patients who had adverse reactions to DTG was 39 years; 68.79% were male, and 31.21% were female. Of the adverse reactions reported, 50.39% were considered persistent. The 3 most frequent reactions were nausea (13.34%), diarrhea (9.83%), and headaches (9.23%). The Brazilian experience with this project has been deemed successful by federal and local managers, and the online tool to collect data has proved to be an important strategy for the pharmacovigilance of DTG as well as that of other drugs.
rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment

Human rDNA clusters form numerous contacts with different chromosomal regions as evidenced by chromosome conformation capture data. Heterochromatization of rDNA genes leads to heterochromatization in different chromosomal regions coupled with the activation of the transcription of genes related to differentiation. These data suggest a role for rDNA clusters in the regulation of many human genes. However, the genes that reside within the rDNA-contacting regions have not been identified. The purpose of this study was to detect and characterize the regions where rDNA clusters make frequent contacts and to identify and categorize genes located in these regions. We analyzed the regions that contact rDNA using 4C data and show that these regions are enriched with genes specifying transcription factors and non-coding RNAs involved in differentiation and development. The rDNA-contacting genes are involved in neuronal development and are associated with different cancers. Heat shock treatment led to dramatic changes in the pattern of rDNA-contacting sites, especially in the regions possessing long stretches of H3K27ac marks. Whole-genome analysis of rDNA-contacting sites revealed specific epigenetic marks and the transcription sites of 20–100 nt non-coding RNAs in these regions. The rDNA-contacting genes jointly regulate many genes that are involved in the control of transcription by RNA polymerase II and the development of neurons. Our data suggest a role for rDNA clusters in the differentiation of human cells and carcinogenesis.
The Catcher in the Field: A Fieldprint based Spoofing Detection for Text-Independent Speaker Verification

Verifying the identity of voice inputs is important as voices are increasingly used for sensitive operations. Traditional methods focus on differentiating individuals via the spectrographic features of voices (e.g., voiceprint), yet cannot cope with spoofing attacks, whereby a malicious attacker synthesizes the voice with almost the same voiceprint of a victim or simply replays it. This paper proposes CaField, a text-independent speaker verification method to detect loudspeaker-based voice spoofing attacks with the goal of achieving two seemingly conflicting requirements: usability and security. The key insight of CaField is to construct "fieldprint'' with the acoustic biometrics embedded in sound fields, i.e., a physical field of acoustic energy created as the sound propagates over the air, as analogous to "voiceprint''. We find that fieldprints can be distinctive between speakers (either humans or loudspeakers), and thus we may detect the speakers being used for spoofing attacks from the authentic users. Our evaluation on a dataset of 20 people and 8 loudspeakers shows that by relying on two on-board microphones to sample sound fields while users talk to the smartphones, CaField achieves a detection accuracy of 99.16% and an equal error rate (EER) of 0.85% across multiple sessions and various voice inputs. CaField supports low audio sample rates at 8~kHz and is robust to various factors including phone displacement, user posture, recording environment, etc.
Next-generation sequencing-guided identification and reconstruction of antibody CDR combinations from phage selection outputs

Abstract Next-generation sequencing (NGS) technologies have been employed in several phage display platforms for analyzing natural and synthetic antibody sequences and for identifying and reconstructing single-chain variable fragments (scFv) and antigen-binding fragments (Fab) not found by conventional ELISA screens. In this work, we developed an NGS-assisted antibody discovery platform by integrating phage-displayed, single-framework, synthetic Fab libraries. Due to limitations in attainable read and amplicon lengths, NGS analysis of Fab libraries and selection outputs is usually restricted to either VH or VL. Since this information alone is not sufficient for high-throughput reconstruction of Fabs, we developed a rapid and simple method for linking and sequencing all diversified CDRs in phage Fab pools. Our method resulted in a reliable and straightforward platform for converting NGS information into Fab clones. We used our NGS-assisted Fab reconstruction method to recover low-frequency rare clones from phage selection outputs. While previous studies chose rare clones for rescue based on their relative frequencies in sequencing outputs, we chose rare clones for reconstruction from less-frequent CDRH3 lengths. In some cases, reconstructed rare clones (frequency ∼0.1%) showed higher affinity and better specificity than high-frequency top clones identified by Sanger sequencing, highlighting the significance of NGS-based approaches in synthetic antibody discovery.
Two new species of the genus Milnesium Doyère, 1840 (Tardigrada, Apochela, Milnesiidae) from Madagascar

Abstract The knowledge of the diversity and distribution of tardigrades on Madagascar is rather poor. To date, only 13 tardigrade taxa have been reported from this region (including one Milnesium species). We examined 46 specimens belonging to two new-to-science species of the genus Milnesium described herein using an integrative approach, including classical morphology and molecular marker (COI, ITS-2 and 28S rRNA) analysis. The species were found in two moss and lichen samples collected in the Ivohibory forest in Fianarantsoa Province. Milnesium matheusisp. nov., with claw configuration [3-3]–[3-3] and rather wide buccal tube, morphologically is most similar to: Mil. beatae Roszkowska, Ostrowska & Kaczmarek, 2015, Mil. bohleberi Bartels, Nelson, Kaczmarek & Michalczyk, 2014, Mil. eurystomum Maucci, 1991, Mil. shilohae Meyer, 2015 and Mil. tumanovi Pilato, Sabella & Lisi, 2016; however, it differs from these by morphometric characteristics. Milnesium wrightaesp. nov., by the presence of four points on secondary branches of claws IV, is most similar to Mil. quadrifidum Nederström, 1919. However, Mil. wrightaesp. nov. differs from Mil. quadrifidum by claw configuration ([4-4]–[4-4] in Mil. quadrifidum vs. [3-3]–[4-4] in Mil. wrightaesp. nov.), but also by the position of the fourth points on secondary branches of claws IV, which are located near the base of the claw in the new species and near the top of the claw in Mil. quadrifidum. Genotypic analysis showed that Mil. matheusisp. nov. is most similar to Milnesium sp. (28S rRNA), Mil. variefidum (COI) and Mil. t. tardigradum (ITS-2) while Mil. wrightaesp. nov. is most similar to Milnesium sp. (28S rRNA), Mil. variefidum (COI) and Mil. matheusi (ITS-2). Five Milnesium taxa are recorded from the African region, including the two new species from Madagascar reported in this study.
Development and growth of the pectoral girdle and fin skeleton in the extant coelacanth Latimeria chalumnae

The monobasal pectoral fins of living coelacanths and lungfishes are homologous to the forelimbs of tetrapods and are thus critical to investigate the origin thereof. However, it remains unclear whether the similarity in the asymmetrical endoskeletal arrangement of the pectoral fins of coelacanths reflects the evolution of the pectoral appendages in sarcopterygians. Here, we describe for the first time the development of the pectoral fin and shoulder girdle in the extant coelacanth Latimeria chalumnae, based on the tomographic acquisition of a growth series. The pectoral girdle and pectoral fin endoskeleton are formed early in development with a radially outward growth of the endoskeletal elements. The visualization of the pectoral girdle during development shows a reorientation of the girdle between the fetus and pup 1 stages, creating a contact between the scapulocoracoids and the clavicles in the ventro‐medial region. Moreover, we observed a splitting of the pre‐ and post‐axial cartilaginous plates in respectively pre‐axial radials and accessory elements on one hand, and in post‐axial accessory elements on the other hand. However, the mechanisms involved in the splitting of the cartilaginous plates appear different from those involved in the formation of radials in actinopterygians. Our results show a proportional reduction of the proximal pre‐axial radial of the fin, rendering the external morphology of the fin more lobe‐shaped, and a spatial reorganization of elements resulting from the fragmentation of the two cartilaginous plates. Latimeria development hence supports previous interpretations of the asymmetrical pectoral fin skeleton as being plesiomorphic for coelacanths and sarcopterygians.
The association between psychological distress and angina pectoris: A population-based study

Background Psychological distress is an undifferentiated combination of symptoms that may be related to the occurrence of angina pectoris (AP). However, few studies have investigated the relationship between psychological distress and AP, particularly in Asian populations. The purpose of this study was to examine the relationship between psychological distress and AP in Taiwanese adults. Methods We adopted a cross-sectional design to explore the data of the 2005–2008 Nutrition and Health Survey in Taiwan. In total, 2080 subjects (aged ≥ 19 years) responded to questionnaire interviews and underwent physical examinations. Each of the five dimensions of psychological distress (sleep disturbance, anxiety, hostility, depression, and feelings of inferiority) were scored (from 0–20) according to the Five-Item Brief Symptom Rating Scale (BSRS-5). A score ≥ 6 points indicated psychological distress. AP was evaluated using a modified Rose questionnaire. Findings In total, 102 subjects (3.6%) had AP, and 231 subjects (8.8%) had symptoms of psychological distress. After adjusting for the basic data, metabolism, and lifestyle covariates, the BSRS-5 total score was associated with AP (odds ratio [OR] = 1.2, 95% confidence interval [CI] = 1.13–1.26, p < 0.001). Subjects with psychological distress had a higher risk of AP (OR = 2.97, 95% CI = 1.76–4.99, p < 0.001). Conclusions The presence of AP is associated with psychological distress. Health care providers should therefore be aware of the impact of psychological distress on AP. Our study findings can serve as a reference for AP assessments. Large scale longitudinal studies are needed to confirm a causal relationship between psychological distress and AP.
Participation, Meaningful Activity, and Social Support Among U.S. Student Service Members/Veterans

Student service members/veterans (SSM/Vs) may experience diminished social support and meaningful activity due to health-related sequelae, in turn threatening their community reintegration. Social and community participation may foster both social support and meaningful activity. This study assessed whether social and community participation explained social support and meaningful activity and evaluated the psychometric properties of the Veterans’ Social and Community Participation Assessment (VSCPA). Online surveys generated responses to the VSCPA, indicators of social support, meaningful activity, health-related challenges, and demographic characteristics. Multiple regression models explored predictors of social support and meaningful activity. The VSCPA comprised three components: active community participation, familial and household participation, and social participation. These components exhibited positive associations with social support and meaningful activity and negative relationships with health-related sequelae. Targeting social and community participation among SSM/Vs may be a fruitful means by which occupational therapists bolster social support and meaningful activity.
Fine‐scale substrate heterogeneity in green roof plant communities: The constraint of size

Abstract Heterogeneity–diversity relationship (HDR) is commonly shown to be positive in accordance with classic niche processes. However, recent soil‐based studies have often found neutral and even negative HDRs. Some of the suggested reasons for this discrepancy include the lack of resemblance between manipulated substrate and natural settings, the treated areas not being large enough to contain species' root span, and finally limited‐sized plots may not sustain focal species’ populations over time. Vegetated green roofs are a growing phenomenon in many cities that could be an ideal testing ground for this problem. Recent studies have focused on the ability of these roofs to sustain stable and diverse plant communities and substrate heterogeneity that would increase niches on the roof has been proposed as a method to attain this goal. We constructed an experimental design using green roof experimental modules (4 m2) where we manipulated mineral and organic substrate component heterogeneity in different subplots (0.25 m2) within the experimental module while maintaining the total sum of mineral and organic components. A local annual plant community was seeded in the modules and monitored over three growing seasons. We found that plant diversity and biomass were not affected by experimentally created substrate heterogeneity. In addition, we found that different treatments, as well as specific subplot substrates, had an effect on plant community assemblages during the first year but not during the second and third years. Substrate heterogeneity levels were mostly unchanged over time. The inability to retain plant community composition over the years despite the maintenance of substrate differences supports the hypothesis that maintenance of diversity is constrained at these spatial scales by unfavorable dispersal and increased stochastic events as opposed to predictions of classic niche processes.
Green tea–induced epigenetic reactivation of tissue inhibitor of matrix metalloproteinase‐3 suppresses prostate cancer progression through histone‐modifying enzymes

Green tea polyphenols (GTPs) and their major constituent, epigallocatechin‐3‐gallate (EGCG), have been reported to demonstrate many interesting biological activities, including anticancer properties. Recent studies on prostate cancer provide strong evidence that epigenetic mechanisms are major players in the regulation of matrix metalloproteinases (MMPs) and their binding partner tissue inhibitor of MMPs (TIMPs) involved in prostate cancer progression. Here we demonstrate that GTP/EGCG mediate epigenetic reactivation of TIMP‐3 that plays a key role in suppressing invasiveness and cancer progression. Treatment of human prostate cancer DUPRO and LNCaP cells with 10 µg/mL GTP and 20 µM EGCG induced TIMP‐3 mRNA and protein expression. This transcriptional activation of TIMP‐3 was associated with the decrease in the expression of both enhancers of zeste homolog 2 (EZH2) and its catalytic product trimethylation of histone H3 at lysine 27 (H3K27me3) repressive marks at the TIMP‐3 promoter with an accompanying increase in histone H3K9/18 acetylation. In addition, GTP/EGCG treatment significantly reduced class I histone deacetylase (HDAC) activity/expression and EZH2 and H3K27me3 levels in prostate cancer cells. EGCG/GTP exposure also reduced MMP‐2/MMP‐9 gelatinolytic activity and abrogated invasion and migration capabilities in these cells. Silencing of EZH2 and class I HDACs strikingly increased the expression of TIMP‐3 independent of DNA methylation. Furthermore, clinical trials performed on patients undergoing prostatectomy consuming 800 mg EGCG (Polyphenon E) up to 6 weeks and grade‐matched controls demonstrate an increase in plasma TIMP‐3 levels. A marked reduction in class I HDACs activity/expression and EZH2 and H3K27me3 levels were noted in GTP‐supplemented prostate tissue. Our findings highlight that TIMP‐3 induction, as a key epigenetic event modulated by green tea in restoring the MMP:TIMP balance suppresses prostate cancer progression.
Effects of Acceptance and Commitment Therapy on Impulsive Decision-Making

This study examined the transdiagnostic effect of acceptance and commitment therapy (ACT) on impulsive decision-making in a community sample. A total of 40 adults were randomized to eight individual sessions of ACT or an inactive control. Participants completed pre-, mid-, and post-assessments for psychological symptoms; overall behavior change; valued living; delay discounting; psychological flexibility; and distress tolerance. Data were analyzed with multilevel modeling of growth curves. Significant interaction effects of time and condition were observed for psychological flexibility, distress tolerance, psychological symptoms, and the obstruction subscale of valued living. No significant interaction effect was found for two delay discounting tasks nor the progress subscale of valued living. The ACT condition had a significantly larger reduction of problem behavior at post-assessment. The results support use of ACT as a transdiagnostic treatment for impulsive behaviors. The lack of change in delay discounting contrasts previous research.
TBAJ-876 Displays Bedaquiline-Like Mycobactericidal Potency without Retaining the Parental Drug’s Uncoupler Activity

The diarylquinoline F1FO-ATP synthase inhibitor bedaquiline (BDQ) displays protonophore activity. Thus, uncoupling electron transport from ATP synthesis appears to be a second mechanism of action of this antimycobacterial drug. Here, we show that the new BDQ analogue TBAJ-876 did not retain the parental drug’s protonophore activity. Comparative time-kill analyses revealed that both compounds exert the same bactericidal activity. ABSTRACT The diarylquinoline F1FO-ATP synthase inhibitor bedaquiline (BDQ) displays protonophore activity. Thus, uncoupling electron transport from ATP synthesis appears to be a second mechanism of action of this antimycobacterial drug. Here, we show that the new BDQ analogue TBAJ-876 did not retain the parental drug’s protonophore activity. Comparative time-kill analyses revealed that both compounds exert the same bactericidal activity. These results suggest that the uncoupler activity is not required for the bactericidal activity of diarylquinolines.