Miracle-dz/UniFAR-FTUs huggingface dataset:
Attraction-Repulsion Spectrum in Neighbor Embeddings

Neighbor embeddings are a family of methods for visualizing complex high-dimensional datasets using $k$NN graphs. To find the low-dimensional embedding, these algorithms combine an attractive force between neighboring pairs of points with a repulsive force between all points. One of the most popular examples of such algorithms is t-SNE. Here we empirically show that changing the balance between the attractive and the repulsive forces in t-SNE using the exaggeration parameter yields a spectrum of embeddings, which is characterized by a simple trade-off: stronger attraction can better represent continuous manifold structures, while stronger repulsion can better represent discrete cluster structures and yields higher $k$NN recall. We find that UMAP embeddings correspond to t-SNE with increased attraction; mathematical analysis shows that this is because the negative sampling optimisation strategy employed by UMAP strongly lowers the effective repulsion. Likewise, ForceAtlas2, commonly used for visualizing developmental single-cell transcriptomic data, yields embeddings corresponding to t-SNE with the attraction increased even more. At the extreme of this spectrum lie Laplacian Eigenmaps. Our results demonstrate that many prominent neighbor embedding algorithms can be placed onto the attraction-repulsion spectrum, and highlight the inherent trade-offs between them.
Damage potential of earthquake ground motions recorded in southern Central America

A total of 18 different components of earthquake ground motion recorded in Central America were selected to conductan evaluation oftheir damage potential. Emphasis was placed in ground motions recorded during recent seismic activity inCosta Rica. For the purpose of comparison, five records obtained in different parts ofthe world were included in the study. Asa mean ofidentif)'ing the damage potential ofthe records, the input energy as well as the plastic hysteretic energy speCtra werecalculated for different levels of displacement ductility and a viscous damping coefficient ~=0.05. The effect of duration ofground motion was studied by introducing the non dimensional parametery and the target ductility μTAR. The parameteryis a function of the maximum displacement and the plastic hysteretic energy dissipation demands. The calculations wereperformed for single-degree-of-freedom systems with an elastoplastic hysteretic behavior. Other response quantities consideredwere the constant strength ductility demands and constant ductility strength demands. The results are contrasted withthe current seismic design recommendations for the region as presented in the latest building codes available.
Permafrost thaw driven changes in hydrology and vegetation cover increase trace gas emissions and climate forcing in Stordalen Mire from 1970 to 2014

Permafrost thaw increases active layer thickness, changes landscape hydrology and influences vegetation species composition. These changes alter belowground microbial and geochemical processes, affecting production, consumption and net emission rates of climate forcing trace gases. Net carbon dioxide (CO2) and methane (CH4) fluxes determine the radiative forcing contribution from these climate-sensitive ecosystems. Permafrost peatlands may be a mosaic of dry frozen hummocks, semi-thawed or perched sphagnum dominated areas, wet permafrost-free sedge dominated sites and open water ponds. We revisited estimates of climate forcing made for 1970 and 2000 for Stordalen Mire in northern Sweden and found the trend of increasing forcing continued into 2014. The Mire continued to transition from dry permafrost to sedge and open water areas, increasing by 100% and 35%, respectively, over the 45-year period, causing the net radiative forcing of Stordalen Mire to shift from negative to positive. This trend is driven by transitioning vegetation community composition, improved estimates of annual CO2 and CH4 exchange and a 22% increase in the IPCC's 100-year global warming potential (GWP_100) value for CH4. These results indicate that discontinuous permafrost ecosystems, while still remaining a net overall sink of C, can become a positive feedback to climate change on decadal timescales. This article is part of a discussion meeting issue ‘Rising methane: is warming feeding warming? (part 2)’.
Airborne quantification of net methane and carbon dioxide fluxes from European Arctic wetlands in Summer 2019

Arctic wetlands and surrounding ecosystems are both a significant source of methane (CH4) and a sink of carbon dioxide (CO2) during summer months. However, precise quantification of this regional CH4 source and CO2 sink remains poorly characterized. A research flight using the UK Facility for Airborne Atmospheric Measurement was conducted in July 2019 over an area (approx. 78 000 km2) of mixed peatland and forest in northern Sweden and Finland. Area-averaged fluxes of CH4 and carbon dioxide were calculated using an aircraft mass balance approach. Net CH4 fluxes normalized to wetland area ranged between 5.93 ± 1.87 mg m−2 h−1 and 4.44 ± 0.64 mg m−2 h−1 (largest to smallest) over the region with a meridional gradient across three discrete areas enclosed by the flight survey. From largest to smallest, net CO2 sinks ranged between −513 ± 74 mg m−2 h−1 and −284 ± 89 mg m−2 h−1 and result from net uptake of CO2 by vegetation and soils in the biosphere. A clear gradient of decreasing bulk and area-averaged CH4 flux was identified from north to south across the study region, correlated with decreasing peat bog land area from north to south identified from CORINE land cover classifications. While N2O mole fraction was measured, no discernible gradient was measured over the flight track, but a minimum flux threshold using this mass balance method was calculated. Bulk (total area) CH4 fluxes determined via mass balance were compared with area-weighted upscaled chamber fluxes from the same study area and were found to agree well within measurement uncertainty. The mass balance CH4 fluxes were found to be significantly higher than the CH4 fluxes reported by many land-surface process models compiled as part of the Global Carbon Project. There was high variability in both flux distribution and magnitude between the individual models. This further supports previous studies that suggest that land-surface models are currently ill-equipped to accurately capture carbon fluxes inthe region. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 2)'.
Mental health support for children and adolescents with hearing loss: scoping review

Background Children with hearing loss are at increased risk of mental health conditions, including behavioural problems, but there is limited evidence about available mental health support. Aims We aimed to map the evidence on mental health support for children and adolescents with hearing loss. Method Medline, Embase, PsycINFO and grey literature databases were searched until April 2021. Articles of any study design were eligible if they described an intervention supporting the mental health of children with hearing loss. No restrictions were placed on geography or publication date. Four reviewers independently screened results by title, abstract and full text. Study characteristics and outcome data were extracted, with results narratively synthesised. Results From 5629 search results, 27 articles were included. A large majority of the studies (81%, n = 22) were from high-income settings, with two-thirds (67%, n = 18) conducted in the USA. Less than half (41%, n = 11) of the articles adopted experimental research designs, and the majority of studies included small samples. The interventions presented were diverse, with the majority either therapy based (30%, n = 8) or skills training (30%, n = 8). Interventions included ice-skating, parent–child interaction therapy and resilience training. When measured, interventions demonstrated at least some evidence of effectiveness, although this was not always assessed with gold-standard methodology. Conclusions The evidence is lacking in breadth, study quality and geographical spread. That said, what is available indicates a range of effective approaches to support the mental health of children with hearing loss. Additional research is needed to improve the breadth of evidence on mental health support for this population.
Deep soft soil improvement by alkaline activation

This research studied the use of alkaline activation of fly ash, as a silica and alumina amorphous source, to improve soft soils. A laboratory programme – including tests to study strength and deformability development, alternative curing methods, the effect of the different components of the grout, effect of raising initial temperature and comparison with a cement grout – was carried out. Laboratory tests revealed that the use of fly ash and alkaline activator resulted in a soil strength improvement up to 11·4, 16·7 and 43·4 MPa, at 28, 90 and 365 days curing, respectively. The most effective combinations obtained in the laboratory were chosen for the field application with jet grouting. The grout performed adequately to pass standard engineering specifications for soil mixing, achieving up to 26·4 MPa at 90 days curing. The main conclusion is the potential of alkaline activation for soil improvement, and therefore this research has created a basis for further studies.
cacna2d3, a voltage-gated calcium channel subunit, functions in vertebrate habituation learning and the startle sensitivity threshold

The ability to filter sensory information into relevant versus irrelevant stimuli is a fundamental, conserved property of the central nervous system and is accomplished in part through habituation learning. Synaptic plasticity that underlies habituation learning has been described at the cellular level, yet the genetic regulators of this plasticity remain poorly understood, as do circuits that mediate sensory filtering. A forward genetic screen for zebrafish genes that control habituation learning identified a mutant allele doryp177 that caused reduced habituation of the acoustic startle response. Whole-genome sequencing identified the calcium voltage-gated channel auxiliary subunit alpha-2/delta-3 (cacna2d3) as a candidate gene affected in doryp177 mutants. Behavioral characterization of larvae homozygous for two additional, independently derived mutant alleles of cacna2d3, together with failure of these alleles to complement doryp177, confirmed a critical role for cacna2d3 in habituation learning. Notably, detailed analyses of the acoustic response in mutant larvae also revealed increased startle sensitivity to acoustic stimuli, suggesting a broader role for cacna2d3 in controlling innate response thresholds to acoustic stimuli. Taken together, our data demonstrate a critical role for cacna2d3 in sensory filtering, a process that is disrupted in human CNS disorders, e.g. ADHD, schizophrenia, and autism.
CD200R Combined Neutrophil-Lymphocyte Ratio Predict 90-Day Mortality in HBV-Related Acute-On-Chronic Liver Failure

Background: Survival of acute-on-chronic liver failure (ACLF) cannot be properly predicted based on clinical characteristics. Aims: This study aimed to develop a predictive model to evaluating the prognosis for hepatitis B virus-related ACLF (HBV-ACLF) based on specific laboratory and immune indicators. Methods: Baseline laboratory results were obtained and immune indicators were detected by flow cytometry. A predictive model, which estimates the prognosis at 90-day follow-up, was developed using data from a prospective study on 45 patients hospitalized of HBV-ACLF from June 2016 to April 2018 at the Beijing Ditan Hospital, Capital Medical University. The prognostic values of the predictive factors were determined by the area under the receiver operating characteristic (AUROC) curves. Results: Six factors exhibited statistical differences between the survival and non-survival groups: proportions of CD4+TN, CD4+TEM, CD8+TN, CD8+TEM, CD200R+CD4+T cells and neutrophil-lymphocyte ratio (NLR). CD200R combined with the NLR had an AUROC of 0.916, which was significantly higher than the AUROC values of CD200R+CD4+T cells (0.868), NLR (0.761), model for end-stage liver disease (MELD) (0.840), MELD-Na (0.870), Child-Turcotte-Pugh (CTP) (0.580), or chronic liver failure-consortium ACLF (CLIF-C ACLF) score(0.840). At the cut-off point of−3.87, matching the maximum Youden index determined by ROC analysis, the positive predictive and negative predictive values for the mortality were 0.86 and 0.97, respectively. Conclusions: The 90-day prediction model based on baseline levels of CD200R+CD4+T cells and NLR offers potential predictive value for the mortality of HBV-ACLF.
Effects of Donepezil and Medroxyprogesterone Versus Placebo on Weaning in Adult Patients With Non-Pulmonary Etiologies Receiving Invasive Mechanical Ventilation: A triple‐blind Randomized Clinical Trial

Background: Medroxyprogesterone and donepezil could be used as respiratory stimulants in ventilated patients. However, no randomized placebo-controlled trial is available to confirm this approach and compare these drugs. The aim of the current study was to evaluate the effects of donepezil or medroxyprogesterone compared to the placebo in improvement in respiratory status and weaning facilitation in critically ill adult patients receiving mechanical ventilation. Material and Methods: This randomized, triple-blind trial was conducted on 78 ventilated patients in intensive care units (ICU). Patients who were intubated due to pulmonary disorders were ruled out. Patients were randomized in a 1:1:1 ratio to receive 5 mg donepezil (n = 23) or 5 mg medroxyprogesterone (n = 26), or placebo (n = 24) twice a day until weaning (maximum 10 days). The primary endpoints were weaning duration, and duration of invasive mechanical ventilation. Secondary endpoints included rate of successful weaning, changes in arterial blood gas (ABG) parameters, GCS and sequential organ failure assessment (SOFA) score, hemoglobin (Hgb), ICU-mortality, and duration of ICU stay, were measured before and after the intervention and if successful weaning was recorded. Results: Of 78 studied patients who were randomized, 59 weaned successfully. 87% patients in donepezil and 88.5% patients in medroxyprogesterone groups were successfully weaned compared to 66.7% patients in the placebo group. However, this difference was not statistically significant (p-Value = 0.111). Changes in pH, mean duration of intubation, and weaning duration were statistically different in donepezil compared with the control group (p-Value < 0.05). No significant difference in ABG, Hgb, GCS and SOFA score, and duration of intubation were seen in the medroxyprogesterone group, but weaning duration was significantly reduced to 1.429 days compared with the control group (p-Value = 0.038). Conclusion: The results of this clinical trial have demonstrated that the administered dose of medroxyprogesterone and donepezil can expedite the weaning process by reducing the weaning duration compared to placebo. Furthermore, the total duration of invasive ventilation was significantly lower in the donepezil group compared to the control group. Future clinical trials with a larger sample size will determine the exact role of medroxyprogesterone and donepezil in mechanically ventilated patients. Clinical Trial Registration: https://irct.ir/IRCT20190810044500N2 (April 1, 2020).
A Direct MS-Based Approach to Profile Human Milk Secretory Immunoglobulin A (IgA1) Reveals Donor-Specific Clonal Repertoires With High Longitudinal Stability

Recently, a mass spectrometry-based approach was introduced to directly assess the IgG1 immunoglobulin clonal repertoires in plasma. Here we expanded upon this approach by describing a mass spectrometry-based technique to assess specifically the clonal repertoire of another important class of immunoglobulin molecules, IgA1, and show it is efficiently and robustly applicable to either milk or plasma samples. Focusing on two individual healthy donors, whose milk was sampled longitudinally during the first 16 weeks of lactation, we demonstrate that the total repertoire of milk sIgA1 is dominated by only 50-500 clones, even though the human body theoretically can generate several orders of magnitude more clones. We show that in each donor the sIgA1 repertoire only changes marginally and quite gradually over the monitored 16-week period of lactation. Furthermore, the observed overlap in clonal repertoires between the two individual donors is close to non-existent. Mothers provide protection to their newborn infants directly by the transfer of antibodies via breastfeeding. The approach introduced here, can be used to visualize the clonal repertoire transferred from mother to infant and to detect changes in-time in that repertoire adapting to changes in maternal physiology.
Two-Phase Flow Performance for Electrical Submersible Pump Stages

Two-phase flow behavior prediction for centrifugal pumps is a difficult task because of the complexity involved in modeling multiphase flow inside turbo machines. An experimental study has been conducted at the U. of Tulsa Artificial Lift Projects (TUALP) with a 513-series, 22-stage, mixed-flow-type pump to gather data for pump performance under two-phase flow conditions. Air and water were used as the working fluids. This study differs from other experimental works because the pressure changes were recorded stage by stage. The results of previous works have been reported as an average of the intake and discharge conditions and depend on the number of stages used. Phenomena such as surging and gas locking were observed during these tests, and their boundaries have been mapped. The pressure increment and total hydraulic horsepower for the average pump, those per stage as a function of the liquid flow rate, and each gas flow rate considered are presented. The pump's average brake horsepower and efficiency also are plotted for the variables mentioned. The results indicate that average pump behavior is significantly different from that observed per stage.
Novel Evidence for the Increasing Prevalence of Unique Names in China: A Reply to Ogihara

In this study, we aimed to address three comments proposed by Ogihara on a recent study where we found that unique names in China have become increasingly popular from 1950 to 2009. Using a large representative sample of Chinese names (N = 2.1 million), we replicated the increase in uniqueness of Chinese names from 1920 to 2005, especially since the 1970s, with multiple uniqueness indices based on name-character frequency and name-length deviation. Over the years, Chinese characters that are rare in daily life or naming practice were more often used in given names, and the length of given names became more deviant from typical practice (i.e., more one-character and three-character given names and higher standard deviation of name length). Taken together, these findings not only reconfirmed the increasing prevalence of unique names but also demonstrated the validity of various indices in assessing name uniqueness in China.
Teachers’ Use of Within-Class Ability Groups in the Primary Classroom: A Mixed Methods Study of Social Comparison

It is common practice within primary classrooms for teachers to spilt children into different ability groups so that children of similar level are taught together. Whilst this practice is used across the globe, research is mixed on the benefits of such grouping strategy. This paper presents data collected from mixed methods research which investigated teachers use of grouping strategies and social comparison, the act of comparing oneself with others. It focuses on when, why and with whom children from different ability groups compare themselves and the impact this has on their self-perceptions. Drawing upon data from children aged between 10 and 11 years from 12 primary schools, social comparison was found to play a significant role in daily classroom life for some children. The study identified different strands of the social comparison process including acknowledgment, topic, target, and direction, and it revealed positive and negative effects of social comparison. A difference by ability group was identified. Children within the low ability group were particularly vulnerable to the negative effects of social comparison and found to engage in more frequent and intentional social comparisons which were heavily relied upon for self-evaluation and performance evaluation. The paper discusses the educational implications of social comparison regarding pupil ability grouping strategies, motivation, engagement, and academic performance. Implications for teacher education and professional development is discussed.
Segmental Abnormalities of White Matter Microstructure in End-Stage Renal Disease Patients: An Automated Fiber Quantification Tractography Study

Background and Purpose: End-stage renal disease (ESRD) results in extensive white matter abnormalities, but the specific damage segment cannot be identified. This study aimed to determine the segmental abnormalities of white matter microstructure in ESRD and its relationship with cognitive and renal function indicators. Methods: Eighteen ESRD patients and 19 healthy controls (HCs) were prospectively recruited. All participants underwent DTI and clinical assessments. Automatic fiber quantification (AFQ) was applied to generate bundle profiles along 16 main white matter tracts. We compared the DTI parameters between groups. Besides, we used partial correlation and multiple linear regression analyses to explore the associations between white matter integrity and cognitive performance as well as renal function indicators. Results: In the global tract level, compared to HCs, ESRD patients had greater MD, AD, and RD values and lower FA value in several fibers (P < 0.05, FDR correction). In the point-wise level, extensive damage existed in specific locations of different fiber tracts, particularly in the left hemisphere (P < 0.05, FDR correction). Among these tracts, the mean AD values of the left cingulum cingulate correlated negatively with MoCA score. Urea and UA level were independent predictors of the AD value of superior component of the left corticospinal. Besides, urea level was the independent predictors of mean MD value of left anterior thalamic radiation (ATR). Conclusion: White matter fiber tract damage in ESRD patients may be characterized by abnormalities in its specific location, especially in the left hemisphere. Aberrational specific located fibers were related to cognitive impairment and renal dysfunction.
Assessment of Knowledge, Attitudes, and Factors Influencing the Selection Student of Generic Medicine

Background: Generic replacements for branded medicines have become a typical practice among registered pharmacists all over the world. Therefore, this study was aimed to determine the influence of the knowledge and attitudes of PharmD students and other factors on the selection of unbranded medicines. Methods: A descriptive, cross-sectional study was conducted through Google Forms to collect data using self-reported questionnaires. The data was collected over a period of 3 months, from January to March 2021, among junior level pharmacy students who are currently undertaking a PharmD course at the King Saud University, College of Pharmacy, Riyadh, Saudi Arabia. Results: The mean age of the students was 21.05± (SD = 1.03), majority of students 70.2% (n = 134) were able to define the term generic medicine, and about 65% (n = 123) were able to correctly define bioequivalence. More than half of the students, 56.5% (n = 108) lacked knowledge about the pharmacokinetic parameters of generic products. Meanwhile, the majority, 85% (n = 122), supported generics over branded medicines, and about 66% (n = 99) agreed that wider use of generic medicines would lead to less money required for the research and development of new pharmaceuticals. Conclusion: Findings revealed that most pharmacy students possess sufficient knowledge of generic medicines, although knowledge in some aspects remains lacking.