Miracle-dz/UniFAR-FTUs huggingface dataset:
Micropopulation mapping of the mouse parafascicular nucleus connections reveals diverse input–output motifs

Introduction In primates, including humans, the centromedian/parafascicular (CM-Pf) complex is a key thalamic node of the basal ganglia system. Deep brain stimulation in CM-Pf has been applied for the treatment of motor disorders such as Parkinson’s disease or Tourette syndrome. Rodents have become widely used models for the study of the cellular and genetic mechanisms of these and other motor disorders. However, the equivalence between the primate CM-Pf and the nucleus regarded as analogous in rodents (Parafascicular, Pf) remains unclear. Methods Here, we analyzed the neurochemical architecture and carried out a brain-wide mapping of the input–output motifs in the mouse Pf at micropopulation level using anterograde and retrograde labeling methods. Specifically, we mapped and quantified the sources of cortical and subcortical input to different Pf subregions, and mapped and compared the distribution and terminal structure of their axons. Results We found that projections to Pf arise predominantly (>75%) from the cerebral cortex, with an unusually strong (>45%) Layer 5b component, which is, in part, contralateral. The intermediate layers of the superior colliculus are the main subcortical input source to Pf. On its output side, Pf neuron axons predominantly innervate the striatum. In a sparser fashion, they innervate other basal ganglia nuclei, including the subthalamic nucleus (STN), and the cerebral cortex. Differences are evident between the lateral and medial portions of Pf, both in chemoarchitecture and in connectivity. Lateral Pf axons innervate territories of the striatum, STN and cortex involved in the sensorimotor control of different parts of the contralateral hemibody. In contrast, the mediodorsal portion of Pf innervates oculomotor-limbic territories in the above three structures. Discussion Our data thus indicate that the mouse Pf consists of several neurochemically and connectively distinct domains whose global organization bears a marked similarity to that described in the primate CM-Pf complex.
TLEs and early VLF events: Simulating the important impact of transmitter‐disturbance‐receiver geometry

Early very low frequency (VLF) events are perturbations to subionospherically propagating VLF radio transmitters which sometimes occur when lightning activity is near the transmitter‐receiver path. They are often correlated to Transient Luminous Events (TLEs). Recent analysis have focused on a new type of early events whose recovery time persists for many minutes, called LOng Recovery Events (LOREs). The underlying cause of these events is still unclear. Curiously, LOREs sometimes appear on only one path, while the same event observed on a different transmitter‐receiver path does not indicate a LORE. In this paper we observe and simulate two cases of early signal perturbations: The first is a typical early VLF event, and the second is a LORE. Both were recorded by two AWESOME VLF receivers in North Africa on 12 December 2009, during the EuroSprite campaign. We combine observations with theoretical modeling to infer the electron density change that most closely reproduces the observed perturbation. Our results explain the cases where LOREs are detected on only one path as resulting from transmitter‐receiver geometry significantly which impacts the modal content and therefore the observed VLF recovery time.
Mark-recapture vs. line-transect abundance estimates of a coastal dolphin population: a case study of Tursiops truncatus from Laguna, southern Brazil

Cetacean populations in coastal habitats are increasingly threatened by multiple anthropogenic impacts. Monitoring these populations to obtain robust estimates of abundance and detect trends over time is critical to achieve conservation goals. Here, we conducted a pilot study to evaluate the effectiveness of two commonly used abundance estimation methods: mark-recapture and distance sampling line-transect. Surveys were conducted to estimate the abundance of bottlenose dolphins in Laguna, southern Brazil. We implemented power-analysis models and compared both techniques in terms of cost, time and effectiveness to detect trends over a five-year period. Mark-recapture models were analyzed in MARK and resulted in an abundance of 50 individuals (CI = 39-64) with a coefficient of variation (CV) of 0.13. The line-transect models were implemented using the program DISTANCE and resulted in an estimate of 62 individuals (CI = 38-103), with a CV of 0.24. Comparing both approaches, mark-recapture resulted 1.30 time more expensive than line-transect for a single season of effort, but was twice as effective in terms of precision. As a consequence, the probability of detecting a 5% trend during a five-year period is 2.08 times higher with mark recapture. Conversely, the final cost to detect a trend with distance sampling is 1.19 time higher but considering six more years of effort. These results highlight the importance of selecting a-priori sampling design techniques that include developing pilot studies that evaluate the bias, precision and accuracy of estimates while considering costs involved. Considering the small population size estimated herein, the sensitivity of both approaches for detecting trends is not sufficient because the original population would be markedly reduced by the time a declining trend was detected. Thus, a precautionary approach is still imperative, even when robust estimates are obtained.
Effect of Propofol, Sevoflurane, and Isoflurane on Postoperative Cognitive Function Following Laparoscopic Cholecystectomy in Elderly Patients

Cognition refers to the mental action or process through which an individual acquires knowledge solvesproblems and makes decisions for the future. In other words, cognition may be defined as themental processes which account for the daily activities carried out by an individual. Deficits in thesemental processes tend to affect the memory, attention, verbal and non-verbal learning, visual andauditory processing, and motor functioning of an individual, thereby resulting in cognitive impairment.Memory is classified into two types, that is, explicit memory and implicit memory. Explicit memoryinvolves the conscious recall of the information received in the past while implicit memory refers to theinformation or knowledge which is unconsciously and effortlessly recalled.
Survivors of the Shoah Visual History Foundation: an introduction to its indexing methodology

Under the guidance of leading scholars and historians the Survivors of the Shoah Visual History Foundation has videotaped the testimonies of Holocaust survivors worldwide in 29 languages. Using state-of-the-art technology a unique indexing system was created to facilitate access to the place names, personal names, events, experiences and other topics in the nearly 50,000 interviews conducted thus far. As studies in indexing multi-media content move forward, the Foundation hopes to create a research center for advancing indexing in the area of digital asset management. This article provides an introduction to the Foundation's unique indexing methodology which has been developed to enable the delivery of survivors' oral testimonies.
Design and Implementation of Adaptive Digital Beamforming Based on FPGA

Adaptive digital beamforming (ADBF) calculates the weight based on specific beamforming algorithms, which hardware implementation generally requires a large number of data computing resources. This paper designs and implements an adaptive digital beamforming system based on FPGA. In the system, the baseband signal is extracted through digital down conversion (DDC); the time-vary weights are calculated through channel equalization, thus generating the weight; finally Weighted summation of data to achieve ADBF. Experimental results show that, the system design is simple and consume slight resources, which has certain engineering application value.
Study on Climatic Differentiation in the South and North Qinling Mountains in Recent 50 Years

As for regionality,the study emphases of global climate change are always in the ecological fragile regions and the transitional zones of physical geographic areas,such as the coastlines,mountains and the gradient zones with sufficient moisture.The Study on climate change in the south and north Qinling Mountains is of important significance in studying global climate change.In this study,the values of mean annual and seasonal temperature and precipitation were calculated based on the data observed by the meteorological stations in the south and north Qinling Mountains so as to analyze the climate change trend from the aspects of temperature and precipitation anomalies,5-year sliding tendency and long-term sliding tendency.In order to investigate the sharp climate change,the Mann-Kendall,sliding T and Yamamoto test method were plied.The results reveal that the average temperature in the south and north Qinling Mountains was in an increase trend,but there was a certain difference in the sharp change time and range: the sharp temperature increase(0.034 ℃/a) in the north Qinling Mountains occurred in 1989,especially in summer and winter,but that(0.014 ℃/a) in the south Qinling Mountains occurred in 1992,especially in summer and winter similarly.Precipitation in the south and north Qinling Mountains was decreased,it was decreased by 2.66 mm/a in the north Qinling Mountains and by 1.36 mm/a in the south Qinling Mountains,respectively,and its reduction was high in summer and autumn in the northern Qinling Mountains but in spring and autumn in the south Qinling Mountains.
Modeling Thermal Stratification in Aquaculture Ponds

A stratification model was developed for the simulation of the temporal and spatial variation of temperature in aquaculture ponds. A new parameter, called the fish turbulent diffusivity, was incorporated in the equation to calculate the diffusion coefficient in this study. A simple, fast, yet robust numerical method was used to solve the equations of the model. The model, programmed in FORTRAN under the frame of the TRNSYS software, was implemented on a microcomputer. Simulation indicated that the fish turbulent diffusivity was important to the heat transfer estimation in aquaculture ponds. The model was tested using temperatures collected from two ponds in the suburbs of Beijing. The determination coefficient between the calculated and measured temperatures was about 0.90, while the standard deviation was about 0.2°C. The model is useful to better understand the evolution of thermal stratification and the process of heat energy and mass transfers in aquaculture ponds.
5. PERIDOTITE DISSOLUTION RATES IN MICROBIAL ENRICHMENT CULTURES

Using peridotite drilled during Ocean Drilling Program Leg 209, a series of enrichment cultures were initiated on board the ship to stimulate microbially enhanced dissolution of olivine. Dissolution was estimated by measured changes in dissolved Li and Si in the media through time (up to 709 days). The results suggest that there was no significant difference between the amounts of dissolved Li and Si in most of the inoculated microbial cultures compared to the control cultures. Alternative explanations for this are that 1. No microbes are living in the culture tubes that can affect the dissolution rates of olivine, 2. The control cultures have microbes effecting the dissolution of olivine as well as the inoculated cultures, 3. Not enough time has passed to build up a large enough microbial population to effect the dissolution of the olivine in the culture tubes, 4. Microbes act to suppress dissolution of olivine instead of enhancing dissolution, and 5. Abiotic dissolution overshadows microbially enhanced dissolution. Further work is required to test these alternatives. 1Josef, J.A. , Fisk, M.R. , and Giovannoni, S. , 2007. Peridotite dissolution rates in microbial enrichment cultures. In Kelemen, P.B. , Kikawa, E. , and Miller, D.J. (Eds.), Proc. ODP, Sci. Results, 209: College Station, TX (Ocean Drilling Program), 1–38. doi:10.2973/odp.proc.sr.209. 002.2007 2Bruce Museum of Arts and Science, 1 Museum Drive, Greenwich CT 068307100, USA. jjosef@brucemuseum.org 3College of Ocean and Atmospheric Sciences, Oregon State University, 104 COAS Administration Building, Corvallis OR 97331-5503, USA. 4Department of Microbiology, Oregon State University, 104 COAS Administration Building, 222 Nash Hall, Corvallis OR 97331-5503, USA. Initial receipt: 7 November 2005 Acceptance: 22 January 2007 Web publication: 6 July 2007 Ms 209SR-002 J.A. JOSEF ET AL. PERIDOTITE DISSOLUTION RATES IN CULTURES 2
Self-Supervised Convolutional Clustering for Picking the First Break of Microseismic Recording

Accurate first break picking is essential for tunnel microseismic monitoring. Here, we propose a self-supervised convolutional clustering picking (SCCP) method for automatically picking the first break of microseismic recordings. The time–frequency features are decomposed and reconstructed using accurate convolutional encoding and decoding under self-supervision. Then, the autoencoder output is unsupervisedly clustered into useful and invalid waveform sections employing the fuzzy $c$ -means (FCMs) algorithm under long short-term memories, global attention, and self-attention constraints. Furthermore, the first point of the useful waveform is determined as the first break. Our results demonstrate that the proposed SCCP method outperforms the short-term average/long-term average (STA/LTA) and Akaike information criterion (AIC). Compared with PhaseNet, a supervised deep-learning method, the SCCP, produces similar performance without using human-labeled data. Practically, when the signal-to-noise ratio (SNR) is reduced to −6 dB, the average mean absolute error and standard deviation of the picking results remain at 1.12 and 9.19 ms, respectively.
Exploring LLM-based Automated Repairing of Ansible Script in Edge-Cloud Infrastructures

Edge-Cloud system requires massive infrastructures located in closer to the user to minimize latencies in handling Big data. Ansible is one of the most popular Infrastructure as Code (IaC) tools crucial for deploying these infrastructures of the Edge-cloud system. However, Ansible also consists of code, and its code quality is critical in ensuring the delivery of high-quality services within the Edge-Cloud system. On the other hand, the Large Langue Model (LLM) has performed remarkably on various Software Engineering (SE) tasks in recent years. One such task is Automated Program Repairing (APR), where LLMs assist developers in proposing code fixes for identified bugs. Nevertheless, prior studies in LLM-based APR have predominantly concentrated on widely used programming languages (PL), such as Java and C, and there has yet to be an attempt to apply it to Ansible. Hence, we explore the applicability of LLM-based APR on Ansible. We assess LLMs’ performance (ChatGPT and Bard) on 58 Ansible script revision cases from Open Source Software (OSS). Our findings reveal promising prospects, with LLMs generating helpful responses in 70% of the sampled cases. Nonetheless, further research is necessary to harness this approach’s potential fully.
Increasing Gene Editing Efficiency via CRISPR/Cas9- or Cas12a-Mediated Knock-In in Primary Human T Cells

T lymphocytes represent a promising target for genome editing. They are primarily modified to recognize and kill tumor cells or to withstand HIV infection. In most studies, T cell genome editing is performed using the CRISPR/Cas technology. Although this technology is easily programmable and widely accessible, its efficiency of T cell genome editing was initially low. Several crucial improvements were made in the components of the CRISPR/Cas technology and their delivery methods, as well as in the culturing conditions of T cells, before a reasonable editing level suitable for clinical applications was achieved. In this review, we summarize and describe the aforementioned parameters that affect human T cell editing efficiency using the CRISPR/Cas technology, with a special focus on gene knock-in.
Can Nicotinamide Adenine Dinucleotide (NAD+) and Sirtuins Be Harnessed to Improve Mare Fertility?

Simple Summary The reproductive capacity of mares has suffered drastically as a result of years of selection based on athletic performance. The world of equine reproduction is now trying to catch up. Recent studies examining niacin deficiencies in women have indicated that nicotinamide adenine dinucleotide (NAD+) is vital for embryo and foetal development, with further animal models showing improvements to oocyte quality with the treatment of NAD+ precursors. Given the enormous benefits shown in these studies, these results show great promise in improving reproductive outcomes in mares. Abstract Years of sire and dam selection based on their pedigree and athletic performance has resulted in a reduction in the reproductive capability of horses. Mare age is considered a major barrier to equine reproduction largely due to an increase in the age at which mares are typically bred following the end of their racing career. Nicotinamide adenine dinucleotide (NAD+) and its involvement in the activation of Sirtuins in fertility are an emerging field of study, with the role of NAD+ in oocyte maturation and embryo development becoming increasingly apparent. While assisted reproductive technologies in equine breeding programs are in their infancy compared to other livestock species such as cattle, there is much more to be learnt, from oocyte maturation to early embryo development and beyond in the mare, which are difficult to study given the complexities associated with mare fertility research. This review examines what is already known about the role of NAD+ and Sirtuins in fertility and discusses how NAD+-elevating agents may be used to activate Sirtuin proteins to improve equine breeding and embryo production programs both in vivo and in vitro.
Tropical cyclone wind field asymmetry—Development and evaluation of a new parametric model

A new parametric model is developed to describe the wind field asymmetry commonly observed in tropical cyclones or hurricanes in a reference frame fixed at its center. Observations from 21 hurricanes from the North Atlantic basin and TC Roger (1993) in the Coral Sea are analyzed to determine the azimuthal and radial asymmetry typical in these mesoscale systems after removing the forward speed. On the basis of the observations, a new asymmetric directional wind model is proposed which adjusts the widely used Holland (1980) axisymmetric wind model to account for the action of blocking high-pressure systems, boundary layer friction, and forward speed. The model is tested against the observations and demonstrated to capture the physical features of asymmetric cyclones and provides a better fit to observed winds than the Holland model. Optimum values and distributions of the model parameters are derived for use in statistical modeling. Finally, the model is used to investigate the asymmetric character of TC systems, including the azimuth of the maximum wind speed, the degree of asymmetry, and the relationship between asymmetry and forward speed.
Antibiotic resistance, plasmids, and virulence-associated markers in human strains of Campylobacter jejuni and Campylobacter coli isolated in Italy

Campylobacteriosis, a prevalent foodborne gastrointestinal infection in Europe, is primarily caused by Campylobacter jejuni and Campylobacter coli, with rising global concerns over antimicrobial resistance in these species. This study comprehensively investigates 133 human-origin Campylobacter spp. strains (102 C. jejuni and 31 C. coli) collected in Italy from 2013 to 2021. The predominant Multilocus Sequence Typing Clonal complexes (CCs) were ST-21 CC and ST-206 CC in C. jejuni and ST-828 CC in C. coli. Ciprofloxacin and tetracycline resistance, mainly attributed to GyrA (T86I) mutation and tet(O) presence, were prevalent, while erythromycin resistance was associated with 23S rRNA gene mutation (A2075G), particularly in C. coli exhibiting multidrug-resistant pattern CipTE. Notable disparities in virulence factors among strains were observed, with C. jejuni exhibiting a higher abundance compared to C. coli. Notably, specific C. jejuni sequence types, including ST-21, ST-5018, and ST-1263, demonstrated significantly elevated counts of virulence genes. This finding underscores the significance of considering both the species and strain-level variations in virulence factor profiles, shedding light on potential differences in the pathogenicity and clinical outcomes associated with distinct C. jejuni lineages. Campylobacter spp. plasmids were classified into three groups comprising pVir-like and pTet-like plasmids families, exhibiting diversity among Campylobacter spp. The study underscores the importance of early detection through Whole Genome Sequencing to identify potential emergent virulence, resistance/virulence plasmids, and new antimicrobial resistance markers. This approach provides actionable public health data, supporting the development of robust surveillance programs in Italy.
Predicting the Invasiveness of Pulmonary Adenocarcinomas in Pure Ground-Glass Nodules Using the Nodule Diameter: A Systematic Review, Meta-Analysis, and Validation in an Independent Cohort

The nodule diameter was commonly used to predict the invasiveness of pulmonary adenocarcinomas in pure ground-glass nodules (pGGNs). However, the diagnostic performance and optimal cut-off values were inconsistent. We conducted a meta-analysis to evaluate the diagnostic performance of the nodule diameter for predicting the invasiveness of pulmonary adenocarcinomas in pGGNs and validated the cut-off value of the diameter in an independent cohort. Relevant studies were searched through PubMed, MEDLINE, Embase, and the Cochrane Library, from inception until December 2022. The inclusion criteria comprised studies that evaluated the diagnostic accuracy of the nodule diameter to differentiate invasive adenocarcinomas (IAs) from non-invasive adenocarcinomas (non-IAs) in pGGNs. A bivariate mixed-effects regression model was used to obtain the diagnostic performance. Meta-regression analysis was performed to explore the heterogeneity. An independent sample of 220 pGGNs (82 IAs and 128 non-IAs) was enrolled as the validation cohort to evaluate the performance of the cut-off values. This meta-analysis finally included 16 studies and 2564 pGGNs (761 IAs and 1803 non-IAs). The pooled area under the curve, the sensitivity, and the specificity were 0.85 (95% confidence interval (CI), 0.82–0.88), 0.82 (95% CI, 0.78–0.86), and 0.73 (95% CI, 0.67–0.78). The diagnostic performance was affected by the measure of the diameter, the reconstruction matrix, and patient selection bias. Using the prespecified cut-off value of 10.4 mm for the mean diameter and 13.2 mm for the maximal diameter, the mean diameter showed higher sensitivity than the maximal diameter in the validation cohort (0.85 vs. 0.72, p < 0.01), while there was no significant difference in specificity (0.83 vs. 0.86, p = 0.13). The nodule diameter had adequate diagnostic performance in differentiating IAs from non-IAs in pGGNs and could be replicated in a validation cohort. The mean diameter with a cut-off value of 10.4 mm was recommended.