Miracle-dz/UniFAR-FTUs huggingface dataset:
Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates

Here we address the problem of the assignment of atom types and bond orders in low molecular weight compounds. For this purpose, we have developed a prediction model based on nonlinear Support Vector Machines (SVM), implemented in a KNOwledge-Driven Ligand Extractor called Knodle, a software library for the recognition of atomic types, hybridization states, and bond orders in the structures of small molecules. We trained the model using an excessive amount of structural data collected from the PDBbindCN database. Accuracy of the results and the running time of our method is comparable with other popular methods, such as NAOMI, fconv, and I-interpret. On the popular Labute's benchmark set consisting of 179 protein-ligand complexes, Knodle makes five to six perception errors, NAOMI makes seven errors, I-interpret makes nine errors, and fconv makes 13 errors. On a larger set of 3,000 protein-ligand structures collected from the PDBBindCN general data set (v2014), Knodle and NAOMI have a comparable accuracy of approximately 3.9% and 4.7% of errors, I-interpret made 6.0% of errors, while fconv produced approximately 12.8% of errors. On a more general set of 332,974 entries collected from the Ligand Expo database, Knodle made 4.5% of errors. Overall, our study demonstrates the efficiency and robustness of nonlinear SVM in structure perception tasks. Knodle is available at https://team.inria. fr/nano-d/software/Knodle .
Neuronal code for extended time in the hippocampus

The time when an event occurs can become part of autobiographical memories. In brain structures that support such memories, a neural code should exist that represents when or how long ago events occurred. Here we describe a neuronal coding mechanism in hippocampus that can be used to represent the recency of an experience over intervals of hours to days. When the same event is repeated after such time periods, the activity patterns of hippocampal CA1 cell populations progressively differ with increasing temporal distances. Coding for space and context is nonetheless preserved. Compared with CA1, the firing patterns of hippocampal CA3 cell populations are highly reproducible, irrespective of the time interval, and thus provide a stable memory code over time. Therefore, the neuronal activity patterns in CA1 but not CA3 include a code that can be used to distinguish between time intervals on an extended scale, consistent with behavioral studies showing that the CA1 area is selectively required for temporal coding over such periods.
Population-based estimate of hepatitis C virus prevalence in Ontario, Canada

Background Hepatitis C virus (HCV) is the most burdensome infectious illness in Canada. Current screening strategies miss a significant proportion of cases, leaving many undiagnosed. Elevated HCV prevalence in those born between 1945 and 1965 has prompted calls for birth-cohort screening in this group. However, Canada lacks population-level data to support this recommendation. We performed a serosurvey to obtain population-based HCV prevalence estimates in Ontario residents born between 1945–1974, to generate evidence for birth-cohort screening recommendations. Methods We tested anonymized residual sera in five-year age-sex bands from Ontario for anti-HCV antibody. We performed descriptive epidemiological analysis and used a logistic regression model to determine HCV risk-factors. Results Of 10,006 sera analyzed, 155 (1.55%, 95% confidence interval (CI) 1.32, 1.81) were positive for HCV antibody. Individuals born between 1950–1964 had a significantly higher combined prevalence of 1.92% (95% CI 1.56, 2.34) compared to 1.14% (95% CI 0.69, 1.77) (p = 0.04) for those born between 1970–1974. For males, comprising 107/155 (69.03%) of positive samples, the highest prevalence was 3.00% (95% CI 1.95, 4.39) for the 1960–1964 birth-cohort. For females, the highest prevalence was 1.56% (95% CI 0.83, 2.65) for those born between 1955–1959. Male sex was significantly associated with positive HCV serostatus. Interpretation HCV prevalence in Ontario is highest among those in this birth cohort, and higher than previous estimates. The prevalence estimates presented in our study provide important data to underpin birth-cohort screening recommendations.
Anterior Temporal Lobe Morphometry Predicts Categorization Ability

Categorization is the mental operation by which the brain classifies objects and events. It is classically assessed using semantic and non-semantic matching or sorting tasks. These tasks show a high variability in performance across healthy controls and the cerebral bases supporting this variability remain unknown. In this study we performed a voxel-based morphometry study to explore the relationships between semantic and shape categorization tasks and brain morphometric differences in 50 controls. We found significant correlation between categorization performance and the volume of the grey matter in the right anterior middle and inferior temporal gyri. Semantic categorization tasks were associated with more rostral temporal regions than shape categorization tasks. A significant relationship was also shown between white matter volume in the right temporal lobe and performance in the semantic tasks. Tractography revealed that this white matter region involved several projection and association fibers, including the arcuate fasciculus, inferior fronto-occipital fasciculus, uncinate fasciculus, and inferior longitudinal fasciculus. These results suggest that categorization abilities are supported by the anterior portion of the right temporal lobe and its interaction with other areas. Highlights Anterior temporal lobe morphometry correlates with categorization performances Semantic is associated with a more rostral temporal region than shape categorization Semantic categorization performances are associated with right temporal connections
Association between sleep apnoea and pulmonary hypertension in Kyrgyz highlanders

This case–control study evaluates a possible association between high altitude pulmonary hypertension (HAPH) and sleep apnoea in people living at high altitude. Ninety highlanders living at altitudes >2500 m without excessive erythrocytosis and with normal spirometry were studied at 3250 m (Aksay, Kyrgyzstan); 34 healthy lowlanders living below 800 m were studied at 760 m (Bishkek, Kyrgyzstan). Echocardiography, polysomnography and other outcomes were assessed. Thirty-six highlanders with elevated mean pulmonary artery pressure (mPAP) >30 mmHg (31–42 mmHg by echocardiography) were designated as HAPH+. Their data were compared to that of 54 healthy highlanders (HH, mPAP 13–28 mmHg) and 34 healthy lowlanders (LL, mPAP 8–24 mmHg). The HAPH+ group (median age 52 years (interquartile range 47–59) had a higher apnoea–hypopnoea index (AHI) of 33.8 events·h−1 (26.9–54.6) and spent a greater percentage of the night-time with an oxygen saturation <90% (T<90; 78% (61–89)) than the HH group (median age 39 years (32–48), AHI 9.0 events·h−1 (3.6–16), T<90 33% (10–69)) and the LL group (median age 40 years (30–47), AHI 4.3 events·h−1 (1.4–12.6), T<90 0% (0–0)); p<0.007 for AHI and T<90, respectively, in HAPH+ versus others. In highlanders, multivariable regression analysis confirmed an independent association between mPAP and both AHI and T<90, when controlled for age, gender and body mass index. Pulmonary hypertension in highlanders is associated with sleep apnoea and hypoxaemia even when adjusted for age, gender and body mass index, suggesting pathophysiologic interactions between pulmonary haemodynamics and sleep apnoea. PH in highland residents is associated with sleep apnoea, suggesting a pathophysiologic interaction http://ow.ly/CQ1k305CQeq
Absence of ethnic differences in the pharmacokinetics of moxifloxacin, simvastatin, and meloxicam among three East Asian populations and Caucasians

Aim To examine whether strict control of clinical trial conditions could reduce apparent differences of pharmacokinetic (PK) parameters among ethnic groups. Methods Open‐label, single dose PK studies of moxifloxacin, simvastatin and meloxicam were conducted in healthy male subjects from three East Asian populations (Japanese, Chinese and Koreans) and one Caucasian population as a control. These three drugs were selected because differences in PK parameters have been reported, even though the backgrounds of these East Asian populations are similar. Moxifloxacin (400 mg) was administered orally to 20 subjects, and plasma and urine levels of moxifloxacin and its metabolite (M2) were measured. Simvastatin (20 mg) was given to 40 subjects, and plasma levels of simvastatin and simvastatin acid were measured. Meloxicam (7.5 mg) was given to 30 subjects and its plasma concentration was determined. Intrinsic factors (polymorphism of UGT1A1 for moxifloxacin, SLCO1B1 for simvastatin, and CYP2C9 for meloxicam) were also examined. Results AUCinf values for moxifloxacin, simvastatin and meloxicam showed no significant differences among the East Asian groups. Cmax values of moxifloxacin and simvastatin, but not meloxicam, showed significant differences. There were no significant differences of data for M2 or simvastatin acid. Genetic analysis identified significant differences in the frequencies of relevant polymorphisms, but these differences did not affect the PK parameters observed. Conclusions Although there were some differences in PK parameters among the three East Asian groups, the present study performed under strictly controlled conditions did not reproduce the major ethnic differences observed in previous studies.
Silane-treated lignocellulosic fibers as reinforcement material in polylactic acid biocomposites

The aim of this research was to study the mechanical and thermal properties of composites based on polylactic acid (PLA) and two types of reinforcements (spent kraft fibers and sisal fibers, with or without modification by silanes). Two different silane coupling agents (3-aminopropyltriethoxysilane and 3-(trimethoxysily)propyl methacrylate) were selected based on previous experiments. Silanization of fibers was measured by ash content, atomic absorption spectroscopy, X-ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM) images. PLA-based composites were manufactured by injection molding, and their thermal and mechanical properties were measured by differential scanning calorimetry (DSC) and by tensile and impact tests, respectively. Composites containing kraft and sisal fibers showed remarkable impact strengths (14.45 J/m and 24.61 J/m, respectively), which were 1.4 and 2.4 times higher than the results achieved with neat PLA probes, respectively. Microscopic analysis revealed a good distribution of reinforcements in the PLA matrix.
Microstructural influences on the growth of small cracks in Ti‐6Al‐4 V

The effects of microstructure on the growth of small cracks in Ti-6Al-4 V under fatigue loading are presented. The small crack growth is compared with large crack growth. Two large crack tests were performed at a stress ratio of 0.4 and a frequency of 15 Hz. For small crack growth tests, double edge notch specimens were loaded under constant amplitude at four maximum stresses with a stress ratio of 0.4 and a frequency of 15 Hz. A plastic replication technique was used to monitor the small fatigue crack growth rate. The microstructure consists of bands of α and β phases. The present study indicates that the crack growth direction and shape are dependent upon the grain size and grain orientations, and that the crack growth rate seems to be affected by the spacing of α-rich and β-rich bands. Small cracks are propagated at stress intensity factors well below the large crack threshold stress intensity factor.
Publication patterns of oral and poster presentations at the annual meetings of the Congress of Neurological Surgeons and the American Association of Neurological Surgeons.

OBJECT National and international meetings, such as the Congress of Neurological Surgeons (CNS) and the American Association of Neurological Surgeons (AANS) meetings, provide a central location for the gathering and dissemination of research. The purpose of this study was to determine the publication rates of both oral and poster presentations at CNS and AANS meetings in peer-reviewed journals. METHODS The authors reviewed all accepted abstracts, presented as either oral or poster presentations, at the CNS and AANS meetings from 2003 to 2005. This information was then used to search PubMed to determine the rate of publication of the abstracts presented at the meetings. Abstracts were considered published if the data presented at the meeting was identical to that in the publication. RESULTS The overall publication rate was 32.48% (1243 of 3827 abstracts). On average, 41.28% of oral presentations and 29.03% of poster presentations were eventually published. Of those studies eventually published, 98.71% were published within 5 years of presentation at the meeting. Published abstracts were published most frequently in the Journal of Neurosurgery and Neurosurgery. CONCLUSIONS Approximately one-third of all presentations at the annual CNS and AANS meetings will be published in peer-reviewed, MEDLINE-indexed journals. These meetings are excellent forums for neurosurgical practitioners to be exposed to current research. Oral presentations have a significantly higher rate of eventual publication compared with poster presentations, reflecting their higher quality. The Journal of Neurosurgery and Neurosurgery have been the main outlets of neurosurgical research from these meetings.
Reconciliation between operational taxonomic units and species boundaries

Abstract The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into operational taxonomic units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for bacterial species. Our results show that the robustness of such a generalised cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene. It will lead to biases in diversity metrics and makes it hard to compare results obtained with amplicons derived with different primer sets. The method introduced within this work takes into account the differential evolutional rates of taxonomic lineages in order to define a dynamic and taxonomic-dependent OTU clustering cut-off score. For a taxonomic family consisting of species showing high evolutionary conservation in the amplified variable regions, the cut-off will be more stringent than 97%. By taking into consideration the amplified variable regions and the taxonomic family when defining this cut-off, such a threshold will lead to more robust results and closer correspondence between OTUs and species. This approach has been implemented in a publicly available software package called DynamiC.
Modelling of temperature dependent impedance in lithium ion polymer batteries and impact analysis on electric vehicles

The objective of this work is to demonstrate a temperature-dependent impedance model for high-power lithium-ion polymer cells used in modern Electric Vehicles (EV). The impedance model is combined with a self-heating thermal model for system simulations, in order to predict the impact of different cell types on the overall EV performance, under real-world urban and highway drive-cycles. Measurements show that the internal resistance is almost doubled when the ambient temperature is lowered from 20° C to 5°C. This has a drastic impact on the EV's ability to satisfy the load current requirements without performance lags, and justifies the importance of the modelling approach. When operating in cold climates, it is observed that the Battery Thermal Management System (BTMS) must strike a balance between EV range and performance, as the stored energy should be optimally distributed between the propulsion and heating systems.
Evidence for a relationship between trait gratitude and prosocial behaviour

ABSTRACT Prosocial behaviour towards unrelated others is communally beneficial but can be individually costly. The emotion of gratitude mitigates this cost by encouraging direct as well as “upstream” reciprocity, thereby facilitating cooperation. A widely used method for measuring trait gratitude is the Gratitude Questionnaire (GQ6) [McCullough, M. , Emmons, R. , & Tsang, J. (2002). The grateful disposition: A conceptual and empirical topography. Journal of Personality and Social Psychology, 82, 112–127. Retrieved from https://doi.org/10.1037/0022-3514.82. 1.112]. Here we undertake an assessment of the external validity of the GQ6 by examining its relationship with two incentivized economic games that serve as face valid indices of generosity and reciprocity. In two studies (total N = 501) we find that trait gratitude as measured by the GQ6 predicts greater donations in a charity donation task as well as greater transfers and returns in an incentivized trust game. These results support the hypothesis that individuals with higher trait gratitude are more generous and trusting on average, and provide initial evidence as to the predictive validity of the GQ6.
Direct single-molecule dynamic detection of chemical reactions

The dynamic process of a nucleophilic addition reaction has been investigated in graphene-molecule single-molecule junctions. Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.
FaultSim

As memory systems scale, maintaining their Reliability Availability and Serviceability (RAS) is becoming more complex. To make matters worse, recent studies of DRAM failures in data centers and supercomputer environments have highlighted that large-granularity failures are common in DRAM chips. Furthermore, the move toward 3D-stacked memories can make the system vulnerable to newer failure modes, such as those occurring from faults in Through-Silicon Vias (TSVs). To architect future systems and to use emerging technology, system designers will need to employ strong error correction and repair techniques. Unfortunately, evaluating the relative effectiveness of these reliability mechanisms is often difficult and is traditionally done with analytical models, which are both error prone and time-consuming to develop. To this end, this article proposes FaultSim, a fast configurable memory-reliability simulation tool for 2D and 3D-stacked memory systems. FaultSim employs Monte Carlo simulations, which are driven by real-world failure statistics. We discuss the novel algorithms and data structures used in FaultSim to accelerate the evaluation of different resilience schemes. We implement BCH-1 (SECDED) and ChipKill codes using FaultSim and validate against an analytical model. FaultSim implements BCH-1 and ChipKill codes with a deviation of only 0.032% and 8.41% from the analytical model. FaultSim can simulate 1 million Monte Carlo trials (each for a period of 7 years) of BCH-1 and ChipKill codes in only 34 seconds and 33 seconds, respectively.
Complications Following Radiofrequency Ablation of Benign Thyroid Nodules: A Systematic Review

Objective: This systematic review examined whether radiofrequency ablation (RFA) is a safe treatment modality for benign thyroid nodules (BTNs). Data Sources: PubMed, Embase, and the Cochrane Library database were searched for articles that (a) targeted human beings and (b) had a study population with BTNs that were confirmed by fine-needle aspiration cytology and/or core needle biopsy. Study Selection: Thirty-two studies relating to 3409 patients were included in this systematic review. Results: Based on literatures, no deaths were associated with the procedure, serious complications were rare, and RFA appears to be a safe and well-tolerated treatment modality. However, a broad spectrum of complications offers insights into some undesirable complications, such as track needle seeding and Horner syndrome. Conclusions: RFA appears to be a safe and well-tolerated treatment modality for BTNs. More research is needed to characterize the complications of RFA for thyroid nodules.
Natural Radionuclide Contents in Raw Materials and the Aggregate Finished Product from Dangote Cement Plc, Obajana, Kogi State, North Central Nigeria

Assessment of gamma ray activity in raw materials and the end product in Dangote Cement from Dangote Cement Plc, Obajana and Kogi State has been investigated in this study. Gamma ray spectrometry that possesses scintillation detector was used to analyze the samples collected from the company. Samples collected as raw materials are limestone, clay, gypsum and laterite and cement as finished product. The 40 K, 238 U, 232 Th activity concentration were detected. The concentration of 40 K range from 4649±366 to 0±65 Bq/Kg with highest value in limestone and lowest in laterite. The 238 U concentration is highest in gypsum range from 696±233 to 41±27 Bq/Kg in laterite. 232 Th activity is below detectable limit in all the raw materials but it has activity concentration of 40±26 Bq/Kg in the finished product which may be traceable to the fact that some finished additives are present which are not in the basic raw materials of this cement under investigation. It is concluded that the natural radionuclide measured for 40 K, 238 U and 232 Th has mean activities of 2189.75±219.5, 331.25±132.25 and 0±31 Bq/Kg respectively, while its corresponding mean absorbed dose rate in air at 1 m above the ground was calculated to be 235.61 nGy/h or 2.064 mSv/y and the aggregate finished product (cement) has absorbed dose rate of 342.22 nGy/h and an effective dose equivalent of 2.998 mSv/y. The calculated absorbed doses in nGy/h and mSv/y shows that Dangote cement under consideration has higher activities of the isotopes than the permissible level suggested by ICRP (80 nGy/h or 0.7 mSv/y)