Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome sequencing of 15 acid-tolerant yeasts

ABSTRACT We report draft genome sequences for 15 non-conventional Saccharomycotina yeast strains obtained from public culture repositories. Included in our collection are eight strains of Pichia with broad tolerance to dicarboxylic acids. The genome sequences of these strains will enable comparative genomics of acid-tolerant phenotypes and strain engineering of non-conventional hosts.
Carbon dynamics, net primary productivity and human‐appropriated net primary productivity across a forest–cocoa farm landscape in West Africa

Terrestrial net primary productivity (NPP) is an important metric of ecosystem functioning; however, there are little empirical data on the NPP of human‐modified ecosystems, particularly smallholder, perennial crops like cocoa (Theobroma cacao), which are extensive across the tropics. Human‐appropriated NPP (HANPP) is a measure of the proportion of a natural system's NPP that has either been reduced through land‐use change or harvested directly and, previously, has been calculated to estimate the scale of the human impact on the biosphere. Additionally, human modification can create shifts in NPP allocation and decomposition, with concomitant impacts on the carbon cycle. This study presents the results of 3 years of intensive monitoring of forest and smallholder cocoa farms across disturbance, management intensity, distance from forest and farm age gradients. We measured among the highest reported NPP values in tropical forest, 17.57 ± 2.1 and 17.7 ± 1.6 Mg C ha−1 year−1 for intact and logged forest, respectively; however, the average NPP of cocoa farms was still higher, 18.8 ± 2.5 Mg C ha−1 year−1, which we found was driven by cocoa pod production. We found a dramatic shift in litterfall residence times, where cocoa leaves decomposed more slowly than forest leaves and shade tree litterfall decomposed considerably faster, indicating significant changes in rates of nutrient cycling. The average HANPP value for all cocoa farms was 2.1 ± 1.1 Mg C ha−1 year−1; however, depending on the density of shade trees, it ranged from −4.6 to 5.2 Mg C ha−1 year−1. Therefore, rather than being related to cocoa yield, HANPP was reduced by maintaining higher shade levels. Across our monitored farms, 18.9% of farm NPP was harvested (i.e., whole cocoa pods) and only 1.1% (i.e., cocoa beans) was removed from the system, suggesting that the scale of HANPP in smallholder cocoa agroforestry systems is relatively small.
Electrochemical detection of a single cytomegalovirus at an ultramicroelectrode and its antibody anchoring

Significance The need for rapid, dependable, and sensitive detection of biological threats is ever increasing. Relatively arduous techniques, with varying degrees of sensitivity, exist for the detection of pathogens, including ELISA, electrogenerated chemiluminescence methods, sensitive PCR techniques, culturing, and microscopy. Here, we extend the observation of particle collisions on ultramicroelectrodes to murine cytomegalovirus. We further present an electrochemical technique for the specific detection of low concentrations of a virus by observing the effect of virus and antibody-specific polystyrene bead binding. This work, in principle, provides a framework for the detection of any biologically relevant antigen. We report observations of stochastic collisions of murine cytomegalovirus (MCMV) on ultramicroelectrodes (UMEs), extending the observation of discrete collision events on UMEs to biologically relevant analytes. Adsorption of an antibody specific for a virion surface glycoprotein allowed differentiation of MCMV from MCMV bound by antibody from the collision frequency decrease and current magnitudes in the electrochemical collision experiments, which shows the efficacy of the method to size viral samples. To add selectivity to the technique, interactions between MCMV, a glycoprotein-specific primary antibody to MCMV, and polystyrene bead “anchors,” which were functionalized with a secondary antibody specific to the Fc region of the primary antibody, were used to affect virus mobility. Bead aggregation was observed, and the extent of aggregation was measured using the electrochemical collision technique. Scanning electron microscopy and optical microscopy further supported aggregate shape and extent of aggregation with and without MCMV. This work extends the field of collisions to biologically relevant antigens and provides a novel foundation upon which qualitative sensor technology might be built for selective detection of viruses and other biologically relevant analytes.
Handbook of North American Indians

My association with Robert F. Heizer and my knowledge of his manner of work and thought, and his personality, was gained in two periods separated by over 20 years. As an undergraduate at Berkeley in the fall of 1948 I was a student in a course he taught, called "The American Indians: Central America, Mexico, and North America. " The wording of the course description sounds as though it may have been several, decades old even then, although one can see now how it might have included ethnohistory: "Development, spread, and attainments of culture; native races and languages. " The texts were Kroeber's (1939) Cultural and Natural Areas and selections from Wissler's (1938) The American Indian. My class notes indicate that the lectures omitted Central America and included little on Mexico. More than two-thirds of the time was devoted to ethnology and culture history. Except for the early archaeology ("peopling"), the material was presented in the then current mode of an essentially timeless "ethnographic preset". I find nothing in my notes that corresponds to modern ethnohistory (except for some discussion of the effects of tbe fur trade on the cultures of the Northwest Coast), and almost no history (except for brief conventional treatment of historic movements onto the Plains and a short account of the introduction of horses). The lectures on California Indians were largely devoted to summaries of Nisenan and Yurok cultures. It was after 1948 that Heizer developed his strong interests in history and ethnohistory, and his realization of the distortions inevitable in attempts to reconstruct a fictional ethnographic present (cf. Heizer 1978b: 4).
Movement of a Large Ice Mass Before Breaking off

Abstract In a two-dimensional model of an ice mass breaking off from a cliff, stresses and velocities are calculated numerically according to Glen's flow law. A tensile crack opens in the zone of maximum tensile principal stress σ1 and propagates to a depth where σ1, iɜ, zero. Ice flow then produces an overhang of the partly detached ice mass. Consequently, the stress σ1 below the tip of the crack becomes tensile again and the crack propagates for another small distance. This process goes on until the centre of gravity of the detaching ice mass has moved past the supporting edge of the bedrock. Velocities v of the ice mass calculated for different stages of the process are plotted as a function of time t. The plotted points lie in the vicinity of a curve given by (1) where vc, tA B and D are constants. The same type of function has been found for velocities measured at an ice mass breaking off the Grubengletscher.
Effect of metformin on the size of the HIV reservoir in non-diabetic ART-treated individuals: single-arm non-randomised Lilac pilot study protocol

Introduction People living with HIV (PLWH) on antiretroviral therapy (ART) do not progress to AIDS. However, they still suffer from an increased risk of inflammation-associated complications. HIV persists in long-lived CD4+ T cells, which form the major viral reservoir. The persistence of this reservoir despite long-term ART is the major hurdle to curing HIV. Importantly, the size of the HIV reservoir is larger in individuals who start ART late in the course of infection and have a low CD4+/CD8+ ratio. HIV reservoir size is also linked to the levels of persistent inflammation on ART. Thus, novel strategies to reduce immune inflammation and improve the host response to control the HIV reservoir would be a valuable addition to current ART. Among the different strategies under investigation is metformin, a widely used antidiabetic drug that was recently shown to modulate T-cell activation and inflammation. Treatment of non-diabetic individuals with metformin controls inflammation by improving glucose metabolism and by regulating intracellular immunometabolic checkpoints such as the adenosin 5 monophosphate activated protein kinase and mammalian target of rapamycin, in association with microbiota modification. Methods and analysis 22 PLWH on ART for more than 3 years, at high risk of inflammation or the development of non-AIDS events (low CD4+/CD8+ ratio) will be recruited in a clinical single-arm pilot study. We will test whether supplementing ART with metformin in non-diabetic HIV-infected individuals can reduce the size of the HIV reservoir as determined by various virological assays. The expected outcome of this study is a reduction in both the size of the HIV reservoir and inflammation following the addition of metformin to ART, thus paving the way towards HIV eradication. Ethics and dissemination Ethical approval: McGill university Health Centre committee number MP-37-2016-2456. Canadian Canadian Institutes of Health Research/Canadian HIV Trials Network (CTN) protocol CTNPT027. Results will be made available through publication in peer-reviewed journals and through the CTN website. Trial registration number NCT02659306
Psychological aftereffects experienced by sexually abused children: Psychopathological characteristics revealed by the K-CBCL

Children who have been sexually abused may experience various short- and long-term psychological sequelae and behavioral problems. This study assessed the mental health of sexually abused children using the Korean-Child Behavior Checklist (K-CBCL) and examined differences from a control group. The participants were 97 children who had been sexually abused and who visited a local Sunflower Center, and 178 control participants. Data were collected via the K-CBCL and analyzed using SPSS version 25.0. T-tests, cross-tabulation, and logistic regression analyses were performed. Scores from the K-CBCL Problem Behavior Syndrome scale were compared between sexually abused children and the control participants. Significant differences were observed between the 2 groups in all the subscales. Compared to the control group, children who were sexually abused showed statistically significant differences in the total problem behavior, internalization, anxiety/depression, withdrawal/depression (withdrawn), somatic symptoms, externalization, rule-breaking behavior (delinquency), aggressive behavior, social immaturity, thought problems, attention problems, and other subscale scores. Sexual violence hurts the overall mental health of children who are abused, including their emotional, behavioral, and social factors. Our findings suggest that multidisciplinary assessment and treatment are required for children who have experienced sexual abuse.
Neuron‐derived extracellular vesicles contain synaptic proteins, promote spine formation, activate TrkB‐mediated signalling and preserve neuronal complexity

Abstract Extracellular vesicles (EVs) play an important role in intercellular communication as carriers of signalling molecules such as bioactive miRNAs, proteins and lipids. EVs are key players in the functioning of the central nervous system (CNS) by influencing synaptic events and modulating recipient neurons. However, the specific role of neuron‐to‐neuron communication via EVs is still not well understood. Here, we provide evidence that primary neurons uptake neuron‐derived EVs in the soma, dendrites, and even in the dendritic spines, and carry synaptic proteins. Neuron‐derived EVs increased spine density and promoted the phosphorylation of Akt and ribosomal protein S6 (RPS6), via TrkB‐signalling, without impairing the neuronal network activity. Strikingly, EVs exerted a trophic effect on challenged nutrient‐deprived neurons. Altogether, our results place EVs in the spotlight for synaptic plasticity modulation as well as a possible therapeutic tool to fight neurodegeneration.
Using a validated instrument to assess pregnancy planning and preconception care at antenatal booking visits: a retrospective cohort study

To determine the completion rate for the London Measure of Unplanned Pregnancy (LMUP), a psychometrically validated measure of a woman's intention with regard to a current or recent pregnancy, during booking visits at two metropolitan antenatal care clinics; to identify socio‐demographic characteristics associated with unplanned pregnancy.
Towards Improved Identification of Vertebral Fractures in Routine Computed Tomography (CT) Scans: Development and External Validation of a Machine Learning Algorithm

Vertebral fractures (VFs) are the hallmark of osteoporosis, being one of the most frequent types of fragility fracture and an early sign of the disease. They are associated with significant morbidity and mortality. VFs are incidentally found in one out of five imaging studies, however, more than half of the VFs are not identified nor reported in patient computed tomography (CT) scans. Our study aimed to develop a machine learning algorithm to identify VFs in abdominal/chest CT scans and evaluate its performance. We acquired two independent data sets of routine abdominal/chest CT scans of patients aged 50 years or older: a training set of 1011 scans from a non‐interventional, prospective proof‐of‐concept study at the Universitair Ziekenhuis (UZ) Brussel and a validation set of 2000 subjects from an observational cohort study at the Hospital of Holbæk. Both data sets were externally reevaluated to identify reference standard VF readings using the Genant semiquantitative (SQ) grading. Four independent models have been trained in a cross‐validation experiment using the training set and an ensemble of four models has been applied to the external validation set. The validation set contained 15.3% scans with one or more VF (SQ2‐3), whereas 663 of 24,930 evaluable vertebrae (2.7%) were fractured (SQ2‐3) as per reference standard readings. Comparison of the ensemble model with the reference standard readings in identifying subjects with one or more moderate or severe VF resulted in an area under the receiver operating characteristic curve (AUROC) of 0.88 (95% confidence interval [CI], 0.85–0.90), accuracy of 0.92 (95% CI, 0.91–0.93), kappa of 0.72 (95% CI, 0.67–0.76), sensitivity of 0.81 (95% CI, 0.76–0.85), and specificity of 0.95 (95% CI, 0.93–0.96). We demonstrated that a machine learning algorithm trained for VF detection achieved strong performance on an external validation set. It has the potential to support healthcare professionals with the early identification of VFs and prevention of future fragility fractures. © 2023 UCB S.A. and The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
Elevation changes of mountain glaciers in the Antarctic Peninsula using ASTER-controlled archival aerial photography

Over the last 50 years a significant increase in the atmospheric and upper ocean temperatures in the Antarctic Peninsula (AP) region has been observed. As a result major ice-shelves have retreated during the 20th century. In connection, glaciers have accelerated and an increased dynamic ice mass loss is observed, especially over the last decade. Despite these major changes, an exact quantification of ice mass changes of the AP, with its roughly 1000 glaciers, is not available. Almost no long-term (multi-decadal) glacier mass balance records for the AP exist and in-situ measurements are rare. On the other hand, the United States Geological Survey (USGS) and British Antarctic Survey (BAS) archives hold a large number of historic aerial stereo-photographs of the AP, dating back to the early 1940s. These images contain a valuable source of information and have been used to demonstrate widespread retreat of glaciers in this region. Less effort has been made so far to use this stereo-photography for the extraction of elevation data to compare it with recent elevation information to determine glacier volume change from which mass changes may be estimated. This dissertation seeks to close this research gap and to extend the number of mass balance records for the AP, by investigating, measuring, and analysing historical glacier elevation change in the AP using digital elevation models (DEMs) derived from USGS and BAS airborne (1948-2005) and ASTER spaceborne (2001-2010) stereo imagery. To ensure reliable and accurate measurements of surface elevation change, extracted DEMs need to be registered in a precise manner. The lack of ground control information in the AP is a major obstacle for this and can result in inaccurate absolute orientations of DEMs. If uncorrected, possible offsets between DEMs introduce significant error and
Rate control protocol (rcp): congestion control to make flows complete quickly

Users typically want their flows to complete as quickly as possible. This makes Flow Completion Time (FCT) an important—arguably the most important—performance metric for the user. Yet research on congestion control focuses entirely on maximizing link throughput, utilization and fairness, which matter more to the operator than the user. This thesis is about a new congestion control algorithm-Rate Control Protocol (RCP)-designed for fast download times (i.e., aka user response times, or flow completion times). Whereas other modifications to (or replacements of) TCP (e.g., STCP, Fast TCP, XCP) are designed to work for specialized applications that use long-lived flows (scientific applications and supercomputer centers), RCP is designed for the typical flows of typical users in the Internet today. We will show that with typical Internet flow sizes, existing (TCP Sack) and newly proposed (XCP) congestion control algorithms make flows last much longer than necessary—often by one or two orders of magnitude. In contrast, RCP makes flows finish close to the minimum possible, leading to a perceptible improvement for web users, distributed computing, and distributed file-systems. We also address several theoretical as well as practical issues under RCP—how RCP's flow completion times compare with TCP, XCP and ideal Processor Sharing, the impact of RCP's short FCTs for the general Internet, stability of an RCP network and how RCP copes with sudden network changes such as flash-crowds, RCP's buffering requirements at routers, implementation of RCP in routers and end-hosts, and how RCP can be incrementally deployed in real networks.
Use (and Misuse) of the Responsible Drinking Message in Public Health and Alcohol Advertising: A Review

The objective is to present a comparative analysis examining the alcohol industry’s and scholarly researchers’ use of the concept “responsible drinking. ” Electronic databases associated with health, education, sociology, psychology, and medicine were the date sources. Results were limited to English, peer-reviewed articles and commentaries specifically addressing “responsible drinking. ” Search descriptors included responsible, responsibility, drinking, alcohol, brewer, and campaign. Eighteen articles constituted the final sample. The matrix method was utilized to organize and abstract pertinent information. Misunderstanding stemming from the inconsistency and counterintuitive nature of brewer-sponsored “responsible drinking” campaigns is further compounded by researchers’ use of the term and concept of “responsible drinking” in their scholarly reports. In articulating the definition of “responsible drinking,” researchers employ subjective notions and personal ideas, thus not differentiating the construct’s meaning from the one acquired in brewer-sponsored campaigns. Researchers are consistently inconsistent when identifying specific health measures that promote and/or contradict responsible alcohol consumption. To evade the subjective notions of researchers and restrictive impressions attached by the alcohol industry, the manner in which individuals interpret, perceive, and practice responsible drinking must be systematically explored and examined using theoretically based constructs.
The Rise of Market Power and the Macroeconomic Implications*

We document the evolution of market power based on firm-level data for the U.S. economy since 1955. We measure both markups and profitability. In 1980, aggregate markups start to rise from 21% above marginal cost to 61% now. The increase is driven mainly by the upper tail of the markup distribution: the upper percentiles have increased sharply. Quite strikingly, the median is unchanged. In addition to the fattening upper tail of the markup distribution, there is reallocation of market share from low- to high-markup firms. This rise occurs mostly within industry. We also find an increase in the average profit rate from 1% to 8%. Although there is also an increase in overhead costs, the markup increase is in excess of overhead. We discuss the macroeconomic implications of an increase in average market power, which can account for a number of secular trends in the past four decades, most notably the declining labor and capital shares as well as the decrease in labor market dynamism.
Study of non-volcanic tremors in the Cascadia subduction zone

The Cascadia subduction zone extends 1,100 km from northern California to southwestern British Columbia. The region is characterized by complicated tectonics due the interactions of three main lithospheric plates: the large Pacific and North American plates and the intervening Juan de Fuca plate system, which includes the Explorer, Juan de Fuca and Gorda plates. The Cascadia subduction zone is thought to be capable of generating megathrust earthquakes at an interval of 500-600 years. The seismogenic portion of the plate interface is mostly offshore and is currently locked, as inferred from geodetic data. However, episodic surface displacements in the direction opposite to the long-term deformation trend, which is caused by relative plate convergence across a locked interface, are observed about every 10 to 19 months, and are accompanied by non-volcanic tremors.
The squall line of 21 July 1992 in southern Germany : An observational case study

On 21 July 1992 a fast moving squall line developed over southwestern Germany and Switzerland in the prefrontal area of a cold front. It moved eastwards and merged with a stationary convergence line ahead of it. The merger occurred in a region where a mesoscale network of 14 automatic weather stations was in operation and it was well documented by the polarimetric Doppler radar at Oberpfaffenhofen near Munchen. In this paper we describe the characteristics of the squall line and its environment based on analyses of the radar and surface data, and on serial radiosonde soundings. The meso-γ-scale features are also described including the gust-front formation and evolution.
A Computationally Practical Simulation Estimator for Panel Data

The author develops a practical extension of D. McFadden's method of simulated moments estimator for limited dependent variable models to the panel data case. The method is based on factorization of the method of simulated moments first order condition into transition probabilities, along with development of an accurate new method for simulating transition probabilities. Monte Carlo tests indicate that this method of simulated moments estimator performs quite well relative to quadrature-based maximum likelihood estimators. It allows estimation of complex panel data models involving random effects and ARMA errors in computational time similar to those necessary for estimation of random effects models via maximum likelihood quadrature. Copyright 1994 by The Econometric Society.