Miracle-dz/UniFAR-FTUs huggingface dataset:
Brevibacillin 2V Exerts Its Bactericidal Activity via Binding to Lipid II and Permeabilizing Cellular Membranes

Lipo-tridecapeptides, a class of bacterial non-ribosomally produced peptides, show strong antimicrobial activity against Gram-positive pathogens, including antibiotic-resistant Staphylococcus aureus and Enterococcus spp. However, many of these lipo-tridecapeptides have shown high hemolytic activity and cytotoxicity, which has limited their potential to be developed into antibiotics. Recently, we reported a novel antimicrobial lipo-tridecapeptide, brevibacillin 2V, which showed no hemolytic activity against human red blood cells at a high concentration of 128 mg/L, opposite to other brevibacillins and lipo-tridecapeptides. In addition, brevibacillin 2V showed much lower cytotoxicity than the other members of the brevibacillin family. In this study, we set out to elucidate the antimicrobial mode of action of brevibacillin 2V. The results show that brevibacillin 2V acts as bactericidal antimicrobial agent against S. aureus (MRSA). Further studies show that brevibacillin 2V exerts its bactericidal activity by binding to the bacterial cell wall synthesis precursor Lipid II and permeabilizing the bacterial membrane. Combined solid-state NMR, circular dichroism, and isothermal titration calorimetry assays indicate that brevibacillin 2V binds to the GlcNAc-MurNAc moiety and/or the pentapeptide of Lipid II. This study provides an insight into the antimicrobial mode of action of brevibacillin 2V. As brevibacillin 2V is a novel and promising antibiotic candidate with low hemolytic activity and cytotoxicity, the here-elucidated mode of action will help further studies to develop it as an alternative antimicrobial agent.
Simulating Subject Communities in Case Law Citation Networks

We propose and evaluate generative models for case law citation networks that account for legal authority, subject relevance, and time decay. Since Common Law systems rely heavily on citations to precedent, case law citation networks present a special type of citation graph which existing models do not adequately reproduce. We describe a general framework for simulating node and edge generation processes in such networks, including a procedure for simulating case subjects, and experiment with four methods of modelling subject relevance: using subject similarity as linear features, as fitness coefficients, constraining the citable graph by subject, and computing subject-sensitive PageRank scores. Model properties are studied by simulation and compared against existing baselines. Promising approaches are then benchmarked against empirical networks from the United States and Singapore Supreme Courts. Our models better approximate the structural properties of both benchmarks, particularly in terms of subject structure. We show that differences in the approach for modelling subject relevance, as well as for normalizing attachment probabilities, produce significantly different network structures. Overall, using subject similarities as fitness coefficients in a sum-normalized attachment model provides the best approximation to both benchmarks. Our results shed light on the mechanics of legal citations as well as the community structure of case law citation networks. Researchers may use our models to simulate case law networks for other inquiries in legal network science.
Analytic and Integrative Framework for Understanding Human Sympathetic Arterial Baroreflex Function: Equilibrium Diagram of Arterial Pressure and Plasma Norepinephrine Level

Background The sympathetic arterial baroreflex is a closed-loop feedback system for stabilizing arterial pressure (AP). Identification of unique functions of the closed system in humans is a challenge. Here we propose an analytic and integrative framework for identifying a static operating point and open-loop gain to characterize sympathetic arterial baroreflex in humans. Methods and Results An equilibrium diagram with two crossing functions of mechanoneural (MN) and neuromechanical (NM) arcs was analyzed during graded tilt maneuvers in seven healthy subjects. AP and plasma norepinephrine level (PNE), as a surrogate for sympathetic nerve activity, and were recorded after vagal modulation of heart function was blocked by atropine. The MN-arc curve was described as a locus of operating points during –7, 0, 15, and 60° head-up tilting (HUT) on a PNE-AP plane. The NM-arc curve was drawn as a line between operating points before and after ganglionic blockade (trimethaphan, 0.1 mg⋅ml–1⋅kg–1) during 0° or 15° HUT. Gain values were estimated from the slopes of these functional curves. Finally, an open-loop gain, which is a most important index for performance of arterial baroreflex, was given by a product of the gain values of MN (GMN) and NM arcs (GNM). Gain values of MN was 8.92 ± 3.07 pg⋅ml−1⋅mmHg−1; and GNM at 0° and 15° HUT were 0.61 ± 0.08 and 0.36 ± 0.05 mmHg⋅ml⋅pg–1, respectively. A postural change from supine to 15° HUT significantly reduced the open-loop gain from 5.62 ± 0.98 to 3.75 ± 0.62. The effects of HUT on the NM arc and open-loop gain seemed to be similar to those of blood loss observed in our previous animal studies. Conclusion An equilibrium-diagram analysis contributes to a quantitative and integrative understanding of function of human sympathetic arterial baroreflex.
Disease Avoidance Model Explains the Acceptance of Cohabitation With Bats During the COVID-19 Pandemic

Bats and humans have a close relationship based on cohabitation, with bats taking roost in buildings. It has been suggested that bats function as a reservoir of the SARS-CoV-2 virus that causes the COVID-19 disease in humans. A misconception that bats can spread SARS-CoV-2 to humans may have increased negative emotions toward bats and reduced individuals’ acceptance of cohabitation with bats during the COVID-19 pandemic. By applying the disease avoidance model, we tested whether knowledge about bats would be associated with reduced negative emotions toward bats, which in turn would be associated with increased acceptance of cohabitation with bats. Moreover, we tested whether previous experiences of bats, perceived COVID-19 risk, age, gender and level of education would be associated with negative emotions and acceptance of bats. A quantitative survey (N = 577) collected during the COVID-19 pandemic in Finland was analyzed with multiple linear regression. The results supported the disease avoidance model. Negative emotions toward bats reduced the acceptance of cohabitation with bats. However, knowledge about bats was associated with increased acceptance of bats both directly, as well as indirectly, via reduced negative emotions. Moreover, perceived COVID-19 risk was associated with increased negative emotions toward bats, and reduced acceptance of bats. Females were more likely than other respondents to report negative emotions, and reduced acceptance of cohabitation with bats. Prior experience of bats was associated with increased acceptance of bats as neighbors. These findings suggest that COVID-19 pandemic may threaten the existence of bats if no action is taken. The findings highlight the importance of correcting misunderstandings about non-human species as transmitters of diseases to humans.
Microbial Diversity and Activity During the Biodegradation in Seawater of Various Substitutes to Conventional Plastic Cotton Swab Sticks

The European Parliament recently approved a new law banning single-use plastic items for 2021 such as plastic plates, cutlery, straws, cotton swabs, and balloon sticks. Transition to a bioeconomy involves the substitution of these banned products with biodegradable materials. Several materials such as polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), poly(butylene succinate) (PBS), polyhydroxybutyrate-valerate (PHBV), Bioplast, and Mater-Bi could be good candidates to substitute cotton swabs, but their biodegradability needs to be tested under marine conditions. In this study, we described the microbial life growing on these materials, and we evaluated their biodegradability in seawater, compared with controls made of non-biodegradable polypropylene (PP) or biodegradable cellulose. During the first 40 days in seawater, we detected clear changes in bacterial diversity (Illumina sequencing of 16S rRNA gene) and heterotrophic activity (incorporation of 3H-leucine) that coincided with the classic succession of initial colonization, growth, and maturation phases of a biofilm. Biodegradability of the cotton swab sticks was then tested during another 94 days under strict diet conditions with the different plastics as sole carbon source. The drastic decrease of the bacterial activity on PP, PLA, and PBS suggested no bacterial attack of these materials, whereas the bacterial activity in PBAT, Bioplast, Mater-Bi, and PHBV presented similar responses to the cellulose positive control. Interestingly, the different bacterial diversity trends observed for biodegradable vs. non-biodegradable plastics allowed to describe potential new candidates involved in the degradation of these materials under marine conditions. This better understanding of the bacterial diversity and activity dynamics during the colonization and biodegradation processes contributes to an expanding baseline to understand plastic biodegradation in marine conditions and provide a foundation for further decisions on the replacement of the banned single-used plastics.
Alternative Measures of Political Efficacy: The Quest for Cross-Cultural Invariance With Ordinally Scaled Survey Items

In this paper, we examine the measurement of citizens’ beliefs that politicians and political systems are responsive (external efficacy) and that citizens see themselves sufficiently skilled to participate in politics (internal efficacy). This paper demonstrates techniques that allow researchers to establish the cross-context validity of conceptually important ordinal scales. In so doing, we show an alternative set of efficacy indicators to those commonly appearing on cross-national surveys to be more promising from a validity standpoint. Through detailed discussion and application of multi-group analysis for ordinal measures, we demonstrate that a measurement model linking latent internal and external efficacy factors performs well in configural and parameter invariance testing when applied to representative samples of respondents in the United States and Great Britain. With near full invariance achieved, differences in latent variable means are meaningful and British respondents are shown to have lower levels of both forms of efficacy than their American counterparts. We argue that this technique may be particularly valuable for scholars who wish to establish the suitability of ordinal scales for direct comparison across nations or cultures.
Escherichia coli O157:H7 in Retail Lettuce (Lactuca sativa) in Addis Ababa City: Magnitude of Contamination and Antimicrobial Susceptibility Pattern

Escherichia coli O157:H7 is an important foodborne pathogen but largely under investigated in Africa. The objectives of this study were to estimate the prevalence and pattern of antimicrobial resistance of E. coli O157:H7 in lettuce in Addis Ababa, Ethiopia. A total of 390 retail lettuce samples were collected across the 10 subcities of Addis Ababa. E. coli O157:H7 was isolated and identified following ISO-16654:2001 standard. The isolates were further tested for antimicrobial susceptibility to 13 antimicrobials using the Kirby–Bauer disk diffusion method. Out of the 390 lettuce samples examined, two (0.51%) carried E. coli O157:H7. The antimicrobial susceptibility pattern of strains showed resistance to ampicillin (100%) and tetracycline (50.0%). One of the two isolates was multidrug resistant to two antimicrobials tested. The results of this study demonstrate the presence of drug-resistant E. coli O157:H7 in lettuce in markets in Addis Ababa. Despite the low prevalence, its presence in a product that is eaten raw highlights potential public health risk in the area associated with this pathogen.
Utility of Huntington's Disease Assessments by Disease Stage: Floor/Ceiling Effects

Introduction: An understanding of the clinimetric properties of clinical assessments, including their constraints, is critical to sound clinical study and trial design. Utilizing data from Enroll-HD—a global, prospective HD observational study and clinical research platform—we examined several well-established HD clinical assessments across all stages of disease for evidence of instrument constraints, specifically floor/ceiling effects, to inform selection of appropriate instruments for use in future studies/trials and identify gaps in instrument utility over the life-course of the disease. Material and Methods: Analyzing publicly available data from 6,614 HD gene-expansion carriers (HDGECs), we grouped participants into deciles based on baseline CAP score, which ranged from 26 to 229. We used descriptive statistics to characterize data distribution for 25 outcome measures (encompassing motor, function, cognition, and psychiatric/behavioral domains) in each CAP decile. A skewness statistic threshold of ±2 was defined a priori to indicate floor/ceiling effects. Results: We found evidence of floor/ceiling effects in the early premanifest stages of disease for most motor and function assessments (e.g., TMS, TFC) and select cognitive tasks (MMSE, Trail Making tests). Other cognitive assessments, and the HADS-SIS scales, performed well ubiquitously, with no evidence of floor/ceiling effects at any disease stage. Floor/ceiling effects were evident at every disease stage for certain assessments, including PBA-s measures. Ceiling effects were apparent for DCL from onset stages onwards, as expected. Discussion: Developing instruments sensitive to subtle differences in performance at the earlier stages of the disease spectrum, particularly in motor and function domains, is warranted.
Dependence on Autophagy for Autoreactive Memory B Cells in the Development of Pristane-Induced Lupus

The production of autoantibodies by autoreactive B cells plays a major role in the pathogenesis of lupus. Increases in memory B cells have been observed in human lupus patients and autoimmune lpr mice. Autophagy is required for the maintenance of memory B cells against viral infections; however, whether autophagy regulates the persistence of autoantigen-specific memory B cells and the development of lupus remains to be determined. Here we show that memory B cells specific for autoantigens can be detected in autoimmune lpr mice and a pristane-induced lupus mouse model. Interestingly, B cell-specific deletion of Atg7 led to significant loss of autoreactive memory B cells and reduced autoantibody production in pristane-treated mice. Autophagy deficiency also attenuated the development of autoimmune glomerulonephritis and pulmonary inflammation after pristane treatment. Adoptive transfer of wild type autoreactive memory B cells restored autoantibody production in Atg7-deficient recipients. These data suggest that autophagy is important for the persistence of autoreactive memory B cells in mediating autoantibody responses. Our results suggest that autophagy could be targeted to suppress autoreactive memory B cells and ameliorate humoral autoimmunity.
Experimental Evidence on the Impact of Payments and Property Rights on Forest User Decisions

Clearing forests for swidden agriculture, despite providing food to millions of farmers in the tropics, can be a major driver of deforestation. Payments for ecosystem services schemes can help stop swidden agriculture-induced forest loss by rewarding forest users for maintaining forests. Clear and secure property rights are a key prerequisite for the success of these payment schemes. In this study, we use a novel iterative and dynamic game in Madagascar and Kenya to examine farmer responses to individual and communal rights to forestlands, with and without financial incentives, in the context of swidden agricultural landscapes. We find that farmer pro conservation behaviour, defined by the propensity to keep forests or fallows on their lands, as well as the effects of land tenure and conservation incentive treatments on such behaviour, differ across the two contexts. The average percentages of land left forest/fallow in the game are 65 and 35% in Kenya and Madagascar, respectively. Individual ownership significantly improves decisions to preserve forests or leave land fallow in Madagascar but has no significant effect in Kenya. Also, the effect of the individual tenure treatment varies across education and wealth levels in Madagascar. Subsidy increases farmers' willingness to support conservation interests in both countries, but its effect is four times greater in Kenya. We find no interaction effects of the two treatments in either country. We conclude that the effectiveness of financial incentives for conservation and tenure reform in preserving forestland vary significantly across contexts. We show how interactive games can help develop a more targeted and practical approach to environmental policy.
Exploring the Origin and Relatedness of Maternal Lineages Through Analysis of Mitochondrial DNA in the Holstein Horse

Maternal lineages are important for the breeding decision in the Holstein horse breed. To investigate the genetic diversity of the maternal lineages and the relationships between founder mares, the maternal inherited mitochondrial genome (except the repetitive part of the non-coding region) of 271 mares representing 75 lineages was sequenced. The sequencing predominantly revealed complete homology in the nucleotide sequences between mares from one lineage with exceptions in 13 lineages, where differences in one to three positions are probably caused by de novo mutations or alternate fixation of heteroplasmy. We found 78 distinct haplotypes that have not yet been described in other breeds. Six of these occurred in two or three different lineages indicating a common ancestry. Haplotypes can be divided into eight clusters with all mares from one lineage belonging to the same cluster. Within a cluster, the average number of pairwise differences ranged from zero to 16.49 suggesting close maternal relationships between these mares. The results showed that the current breeding population originated from at least eight ancestral founder mares.
Prevalence and Incidence of Sexually Transmitted Infection in Injectable Progestin Contraception Users in South Africa

Introduction: Whether intramuscular depot medroxyprogesterone acetate (DMPA-IM) and norethisterone enanthate (NET-EN) have a differential impact on the incidence of sexually transmitted infection (STI) remains unclear. In the Vaginal and Oral Interventions to Control the Epidemic (VOICE) trial, HIV-1 acquisition was higher for DMPA-IM users vs. NET-EN users. We compared DMPA-IM and NET-EN users with regard to chlamydia, gonorrhea, trichomoniasis, syphilis, and herpes simplex virus type 2 (HSV-2) infection. Materials and Methods: Prospective data were analyzed from VOICE, a randomized trial of HIV-1 chemoprophylaxis. Participants were evaluated annually and as indicated for chlamydia, gonorrhea, trichomoniasis, and syphilis. Stored specimens were tested for HSV-2. Proportional hazards models compared the risk of STI between DMPA-IM and NET-EN users. Results: Among 2,911 injectable contraception users in South Africa, 1,800 (61.8%) used DMPA-IM and 1,111 used NET-EN (38.2%). DMPA-IM and NET-EN users did not differ in baseline chlamydia: 15.1 vs. 14.3%, p = 0.54; gonorrhea: 3.4 vs. 3.7%, p = 0.70; trichomoniasis: 5.7 vs.5. 0%, p = 0.40; or syphilis: 1.5 vs. 0.7%, p = 0.08; but differed for baseline HSV-2: (51.3 vs. 38.6%, p < 0.001). Four hundred forty-eight incident chlamydia, 103 gonorrhea, 150 trichomonas, 17 syphilis, and 48 HSV-2 infections were detected over 2,742, 2,742, 2,783, 2,945, and 756 person-years (py), respectively (chlamydia 16.3/100 py; gonorrhea 3.8/100 py; trichomoniasis 5.4/100 py; syphilis 0.6/100 py; HSV-2 6.4/100 py). Comparing DMPA-IM with NET-EN users, no difference was noted in the incidence of chlamydia, gonorrhea, trichomoniasis, syphilis, or HSV-2 infections, including when adjusted for confounders [chlamydia (aHR 1.03, 95% CI 0.85–1.25), gonorrhea (aHR 0.88, 95% CI 0.60–1.31), trichomoniasis (aHR 1.07, 95% CI 0.74–1.54), syphilis (aHR 0.41, 95% CI 0.15–1.10), and HSV-2 (aHR 0.83, 95% CI 0.45–1.54, p = 0.56)]. Discussion: Among South African participants enrolled in VOICE, DMPA-IM and NET-EN users differed in prevalence of HSV-2 at baseline but did not differ in the incidence of chlamydia, gonorrhea, trichomoniasis, syphilis, or HSV-2 infection. Differential HIV-1 acquisition, previously demonstrated in this cohort, does not appear to be explained by differential STI acquisition. However, the high incidence of multiple STIs reinforces the need to accelerate access to comprehensive sexual and reproductive health services.
Prediction of Second Language Proficiency Based on Electroencephalographic Signals Measured While Listening to Natural Speech

This study had two goals: to clarify the relationship between electroencephalographic (EEG) features estimated while non-native speakers listened to a second language (L2) and their proficiency in L2 determined by a conventional paper test and to provide a predictive model for L2 proficiency based on EEG features. We measured EEG signals from 205 native Japanese speakers, who varied widely in English proficiency while they listened to natural speech in English. Following the EEG measurement, they completed a conventional English listening test for Japanese speakers. We estimated multivariate temporal response functions separately for word class, speech rate, word position, and parts of speech. We found significant negative correlations between listening score and 17 EEG features, which included peak latency of early components (corresponding to N1 and P2) for both open and closed class words and peak latency and amplitude of a late component (corresponding to N400) for open class words. On the basis of the EEG features, we generated a predictive model for Japanese speakers’ English listening proficiency. The correlation coefficient between the true and predicted listening scores was 0.51. Our results suggest that L2 or foreign language ability can be assessed using neural signatures measured while listening to natural speech, without the need of a conventional paper test.