Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil ecology along an urban to rural gradient in the southern Appalachians

The urban gradient paradigm was used to investigate the influence of the urban environment on soils in Asheville, NC. A transect of forested plots was established from Asheville, NC to the Pisgah National Forest. The objectives of this study were to: (1) characterize the nature of the urban to rural land use gradient,(2) determine the response of soil physical and chemical properties to an urban environment, (3) characterize the response of the soil nematode community to an urban environment (as an indicator of the soil food web), and (4) determine if urban influences on the soil physical, chemical, and biological environment translate into measurable ecosystem effects. Soil chemical and physical properties were monitored along the gradient. Urban influences on the soil environment were observed. Urban soils were drier, had less organic matter content and were warmer than rural soils along the transect. The soil nematode community assemblage was observed along the gradient. Nematode diversity was not affected by the urban environment. However, the functional composition of the nematode community was influenced by the urban environment. Predatory and omnivorous nematodes were less abundant in the urban soils. Total nematode abundance was also lower in the urban soils. Maturity indices of the nematode community did not strongly reflect this change in the trophic composition of the community. Two ecosystem processes were monitored in this study, leaf litter decomposition and net nitrogen mineralization. The decomposition rate of a standard leaf litter (Quercus prinus) was slower in the urban plots, as evidenced by the ash-free dry mass remaining in the litter through time and the calculated rate constant. Net Nmineralization rates were greater in the urban soils. While litter decomposition rates were not correlated with soil environmental variables, rates of net N-mineralization were influenced by both the soil physical environment and the composition of the nematode community along the urban gradient. INDEX WORDS: Urban ecology, Gradient, Soil chemistry, Nematodes, Maturity Index, Decomposition, N-mineralization SOIL ECOLOGY ALONG AN URBAN TO RURAL GRADIENT IN THE SOUTHERN APPALACHIANS
Interferon-α receptor antisense oligonucleotides reduce neuroinflammation and neuropathology in a mouse model of cerebral interferonopathy

Chronic and elevated levels of the antiviral cytokine IFN-α in the brain are neurotoxic. This is best observed in patients with genetic cerebral interferonopathies such as Aicardi-Goutières syndrome. Cerebral interferonopathies typically manifest in early childhood and lead to debilitating disease and premature death. There is no cure for these diseases with existing treatments largely aimed at managing symptoms. Thus, an effective therapeutic strategy is urgently needed. Here, we investigated the effect of antisense oligonucleotides targeting the murine IFN-α receptor (Ifnar1 ASOs) in a transgenic mouse model of cerebral interferonopathy. Intracerebroventricular injection of Ifnar1 ASOs into transgenic mice with brain-targeted chronic IFN-α production resulted in a blunted cerebral interferon signature, reduced neuroinflammation, restoration of blood-brain barrier integrity, absence of tissue destruction, and lessened neuronal damage. Remarkably, Ifnar1 ASO treatment was also effective when given after the onset of neuropathological changes, as it reversed such disease-related features. We conclude that ASOs targeting the IFN-α receptor halt and reverse progression of IFN-α–mediated neuroinflammation and neurotoxicity, opening what we believe to be a new and promising approach for the treatment of patients with cerebral interferonopathies.
REE Content and Distribution in Apatite and Its Geological Tracing Significance

Apatite is one of the most widespread minerals in nature and it can be found almost in all types of igneous rocks, as well as in metamorphic rocks, sedimentary, and some ore deposits. The chemical formula of apatite is A_5(XO_4)_3(F,OH,Cl),where A represents Ca, REE, Mn, Sr, etc.; X stands for P, As, V, Si, S, C, etc. More or less REE are contained in apatite, with the maximum value up to 11.14%. The REE in the crystal structure of apatite replace Ca while Ca occupies two sites in the lattice (nine coordinated and seven coordinated, respectively). So the apatite can host various rare earth element,As compared with the selective-assemblage minerals apatite is more suitable to use as a indicator mineral to reflect the REE characteristics of rock- and ore-forming geological environments. Summarized in this paper are the REE compositions and Sr isotopic values (~(87)Sr/~(86)Sr)_I of apatites separated from ultrabasic rocks, basic rocks, intermediate rocks, acid rocks, alkaline rocks, carbonatite, granopegmatite, phosphorite and some ore deposits. The results have shown that there are significant differences in chondrite-normalized REE distribution patterns for apatites differing in the mode of occurrence and origin. They can be distinguished from one another by plotting (La/Yb)_N against δEu. For instance, apatites in alkaline rocks and carbonatite possess the highest (La/Yb)_N and δEu values wheres those occurring in granites (especially those granites associated with mineralization of Nb, Ta, W, Sn, Li and Be) have the lowest values. Both (La/Yb)_N and δEu values of apatites from basic and intermediate rocks lie between the above two types. In combination with Sr isotopic measurements in apatite, it is possible to acquire more geological information.
THE VARIATION CHARACTERISTICS FOR TEMPERATURE OF 3 CITIES OF GUANGDONG PROVINCE IN THE PAST ONE HUNDRED YEARS

On the basis of a systematical classification for the temperature data of Guangzhou,Shantou and Macao before 1949,the sequences of temperature variation during the past 100 years for the above three sites were established and the temperature changing features of the southeast coastal area near Guangdong province over the past century were analyzed.The annual average temperature has a rise of 0.61℃,0.62℃,0.43℃ in Guangzhou,Shantou and Macao respectively during the past 100 years,and the increasing range is within the global average scope.The hugest increasing range of temperature in Guangdong province takes place in Spring,and secondly in Winter,which is different from other cities in China,where the rising of temperature happened mainly in Winter. The temperature rise in Guangzhou,Shantou and Macao could be caused by the temperature changing of the highest,the lowest,the highest and the lowest together.Moreover,there existed three circles of 20a,12a and 5a for the above three cities.
Tetramethylpyrazine attenuates renal tubular epithelial cell ferroptosis in contrast-induced nephropathy by inhibiting transferrin receptor and intracellular reactive oxygen species

Abstract Contrast-induced nephropathy (CIN) is a leading cause of hospital-acquired acute kidney injury (AKI). Recently, ferroptosis was reported to be crucial for AKI pathogenesis. Our previous studies indicated antioxidant tetramethylpyrazine (TMP) prevent CIN in vivo. However, whether ferroptosis is involved in TMP nephroprotective mechanism against CIN is unclear. In the present study, we investigated the role of renal tubular epithelial cell ferroptosis in TMP reno-protective effect against CIN and the molecular mechanisms by which TMP regulates ferroptosis. Classical contrast-medium, Iohexol, was used to construct CIN models in rats and HK-2 cells. Results showed that tubular cell injury was accompanied by ferroptosis both in vivo and in vitro, including the typical features of ferroptosis, Fe2+ accumulation, lipid peroxidation and decreased glutathione peroxidase 4 (GPX4). Ferroptosis inhibition by classic inhibitors Fer-1 and DFO promoted cell viability and reduced intracellular ROS production. Additionally, TMP significantly inhibited renal dysfunction, reduced AKI biomarkers, prevented ROS production, inhibited renal Fe2+ accumulation and increased GPX4 expression. Expressions of various proteins associated with iron ion metabolism, including transferrin receptor (TFRC), divalent metal transporter 1, iron-responsive element binding protein 2, ferritin heavy chain 1, ferroportin 1, and heat shock factor binding protein 1, were examined using mechanistic analyses. Among these, TFRC changes were the most significant after TMP pretreatment. Results of siRNA knockdown and plasmid overexpression of TFRC indicated that TFRC is essential for TMP to alleviate ferroptosis and reduce LDH release, Fe2+ accumulation and intracellular ROS. Our findings provide crucial insights about the potential of TMP in treating AKI associated with ferroptosis.
Optimising wound care for patients with cirrhosis: A study of the effect of combination therapy on wound healing

Abstract Cirrhosis, a chronic liver disease, significantly impairs wound healing due to complex alterations in physiology, including compromised immune function, poor nutritional status and altered blood flow. This prospective observational cohort study aimed to evaluate the effectiveness of the multidimensional combination therapy approach in enhancing wound healing among patients diagnosed with cirrhosis. The study was conducted from February to November 2023 in Shanghai, China, including 248 patients with cirrhosis experiencing poor wound healing. The combination therapy consisted of tailored pharmacological treatments, advanced wound dressings, dietitian‐directed dietary regimens and supplementary therapies like negative pressure wound therapy (NPWT), stem cell and hyperbaric oxygen therapy. The interventions were customised based on comprehensive initial assessments of liver function, nutritional status and wound characteristics. Follow‐ups were conducted to monitor response and adjust treatments accordingly. The patient demographic was varied, predominantly 41–60 years old, with the slight male predominance. The study demonstrated that after 3 months of treatment, wound sizes decreased significantly across all cirrhosis severity levels: mild (2.4–1.7 cm2), moderate (4.1–2.6 cm2) and severe (6.2–4.4 cm2). Healing rates improved to 90% in mild, 75% in moderate and 45% in severe cases over 6 months. Albumin levels increased by the average of +0.3 g/dL to +0.4 g/dL post‐treatment across the severity spectrum. However, complication rates escalated with severity: Mild cases had a 10% infection rate, while severe cases had up to 30% infection rate. Combination therapy significantly improved wound healing in cirrhosis patients, with the extent of improvement correlated with the severity of the condition. Tailored, multidisciplinary approaches are critical in managing the intricate wound healing process in cirrhosis, effectively reducing healing times and improving overall treatment outcomes. These findings advocate for personalised care strategies and highlight the potential of integrating various treatment modalities to address the complex needs of this population.
Transcutaneous auricular vagus nerve stimulation ameliorates adolescent depressive‐ and anxiety‐like behaviors via hippocampus glycolysis and inflammation response

Abstract Background Transcutaneous auricular vagus nerve stimulation (taVNS) is a crucial neuromodulation therapy for depression, yet its molecular mechanism remains unclear. Here, we aim to unveil the underlying mechanisms of antidepression by systematically evaluating the change of gene expression in different brain regions (i.e., hippocampus, anterior cingulate cortex, and medial prefrontal cortex). Methods The adolescent depression rat model was established by chronic unpredictable mild stress (CUMS), followed by the taVNS treatment for 3 weeks. The open field test (OFT), forced swimming test (FST), elevated plus maze test (EPM), and new object recognition (NOR) test were used to evaluate depressive‐ and anxiety‐like behaviors. Gene expression analysis of three brain regions was conducted by RNA sequencing (RNA‐seq) and further bioinformatics methods. Results The depressive‐ and anxiety‐like behaviors in CUMS‐exposed rats were manifested by decreased spontaneous locomotor activity of OFT, increased immobility time of FST, increased entries and time in the closed arms of EPM, and decreased new object index of NOR. Furthermore, CUMS exposure also led to alterations in gene expression within the hippocampus (HIP), anterior cingulate cortex (ACC), and medial prefrontal cortex (mPFC), suggesting a potential link between adolescent stress and pathological changes within these brain regions. TaVNS could significantly ameliorate depressive‐ and anxiety‐like behaviors. Its effects on these three brain regions were found related to regulation of the metabolism, and there were some brain region‐specific findings. Compared with ACC and mPFC, taVNS has a more concrete effect on HIP by regulating the inflammation response and glycolysis. Conclusion taVNS is capable of ameliorating adolescent depressive‐ and anxiety‐like behaviors by regulating plenty of genes in the three brain regions. Suppressed level of inflammatory response and enhanced glycolysis manifests the dominant role of taVNS in HIP, which provides a theoretical foundation and data support for the molecular mechanism of antidepression by taVNS.
Dental caries and associated factors among preschool children in Southwest Ethiopia: a cross-sectional study

Background Dental caries is a global public health problem, especially for young children. This study aimed to assess the prevalence of dental caries and its associated factors among preschool children in Mizan Aman town, Southwest Ethiopia. Methods A school-based cross-sectional study was conducted from 1 October to 1 December 2022. A total of 354 children and their parents participated using simple random sampling techniques. Data were collected through an oral clinical examination, interviewing the parents and measuring the anthropometry of the children. Results The prevalence of dental caries was 36.4% (95% CI 31.2% to 41.8%). Night feeding (adjusted OR (AOR)=3.98, 95% CI 1.56 to 10.15), children who did not brush their teeth under parental supervision (AOR=2.98, 95% CI 1.60 to 5.57), body mass index (AOR=3.48, 95% CI 1.30 to 9.41) and history of dental visits (AOR=3.05, 95% CI 1.61 to 5.81) were significantly associated with dental caries. Conclusion The prevalence of dental caries in preschool children was found to be high. Children who did not brush their teeth under parental supervision, who had experience of night feeding, who had a high body mass index and who had a history of dental visits were at risk for dental caries. Prevention of those identified modifiable risk factors should be considered to reduce dental caries.
Probing $Ca_3Ti_2O_7$ crystal structure at the atomic level: Insights from $^{111m}Cd/^{111}Cd$ PAC spectroscopy and ab-initio studies

Perturbed angular correlation spectroscopy combined with $ab-initio$ electronic structure calculations is used to unravel the structural phase transition path from the low-temperature polar structure to the high-temperature structural phase in $Ca_3Ti_2O_7$, a hybrid improper ferroelectric. This procedure explores the unique features of a local probe environment approach by monitoring the evolution of the electric field gradient tensor at the calcium sites. The local environments, observed above 1057 K, confirm a structural phase transition from the $A2_1am$ symmetry to an orthorhombic $Acaa$ symmetry in the $Ca_3Ti_2O_7$ crystal lattice, disagreeing with the frequently reported avalanche structural transition from the polar $A2_1am$ phase to the aristotype $I4/mmm$ phase. Moreover, the EFG temperature dependency, within the $A2_1am$ temperature stability, is shown to be sensitive to the recently proposed $Ca_3Ti_2O_7$ ferroelectric polarization decrease within the 500-800~K temperature range.
Symbolic Solution of Systems of Polynomial Differential Equations Via The Cauchy-Riemann Equations. Applications to Kinetic Differential Equations

The differential equations of chemical kinetics are systems of nonlinear (polynomial) differential equations, therefore their solutions cannot usually be found in symbolic form. Here we offer a method to solve classes of kinetic differential equations based on the Cauchy--Riemann equations. It turns out that the method can be used to symbolically solve some polynomial differential equations that are not necessarily kinetic, as well.
OpenMathInstruct-1: A 1.8 Million Math Instruction Tuning Dataset

Recent work has shown the immense potential of synthetically generated datasets for training large language models (LLMs), especially for acquiring targeted skills. Current large-scale math instruction tuning datasets such as MetaMathQA (Yu et al., 2024) and MAmmoTH (Yue et al., 2024) are constructed using outputs from closed-source LLMs with commercially restrictive licenses. A key reason limiting the use of open-source LLMs in these data generation pipelines has been the wide gap between the mathematical skills of the best closed-source LLMs, such as GPT-4, and the best open-source LLMs. Building on the recent progress in open-source LLMs, our proposed prompting novelty, and some brute-force scaling, we construct OpenMathInstruct-1, a math instruction tuning dataset with 1.8M problem-solution pairs. The dataset is constructed by synthesizing code-interpreter solutions for GSM8K and MATH, two popular math reasoning benchmarks, using the recently released and permissively licensed Mixtral model. Our best model, OpenMath-CodeLlama-70B, trained on a subset of OpenMathInstruct-1, achieves a score of 84.6% on GSM8K and 50.7% on MATH, which is competitive with the best gpt-distilled models. We release our code, models, and the OpenMathInstruct-1 dataset under a commercially permissive license.
FedLion: Faster Adaptive Federated Optimization with Fewer Communication

In Federated Learning (FL), a framework to train machine learning models across distributed data, well-known algorithms like FedAvg tend to have slow convergence rates, resulting in high communication costs during training. To address this challenge, we introduce FedLion, an adaptive federated optimization algorithm that seamlessly incorporates key elements from the recently proposed centralized adaptive algorithm, Lion (Chen et al. 2o23), into the FL framework. Through comprehensive evaluations on two widely adopted FL benchmarks, we demonstrate that FedLion outperforms previous state-of-the-art adaptive algorithms, including FAFED (Wu et al. 2023) and FedDA. Moreover, thanks to the use of signed gradients in local training, FedLion substantially reduces data transmission requirements during uplink communication when compared to existing adaptive algorithms, further reducing communication costs. Last but not least, this work also includes a novel theoretical analysis, showcasing that FedLion attains faster convergence rate than established FL algorithms like FedAvg.
Prediction Challenge: Simulating Rydberg Photoexcited Cyclobutanone with Surface Hopping Dynamics based on Different Electronic Structure Methods

This research examines the nonadiabatic dynamics of cyclobutanone after excitation into the n-3s Rydberg S2 state. It stems from our contribution to the Special Topic of the Journal of Chemical Physics to test the predictive capability of computational chemistry against unseen experimental data. Decoherence-corrected fewest-switches surface hopping (DC-FSSH) was used to simulate nonadiabatic dynamics with full and approximated nonadiabatic couplings. Several simulation sets were computed with different electronic structure methods, including a multiconfigurational wavefunction (MCSCF) specially built to describe dissociative channels, multireference semiempirical approach, time-dependent density functional theory, algebraic diagrammatic construction, and coupled cluster. MCSCF dynamics predicts a slow deactivation of the S2 state (10 ps), followed by an ultrafast population transfer from S1 to S0 (<100 fs). CO elimination (C3 channel) dominates C2H4 formation (C2 channel). These findings radically differ from the other methods, which predicted S2 lifetimes 10 to 250 times shorter and C2 channel predominance. These results suggest that routine electronic structure methods may hold low predictive power for the outcome of nonadiabatic dynamics.
A Framework For Gait-Based User Demography Estimation Using Inertial Sensors

Human gait has been shown to provide crucial motion cues for various applications. Recognizing patterns in human gait has been widely adopted in various application areas such as security, virtual reality gaming, medical rehabilitation, and ailment identification. Furthermore, wearable inertial sensors have been widely used for not only recording gait but also to predict users' demography. Machine Learning techniques such as deep learning, combined with inertial sensor signals, have shown promising results in recognizing patterns in human gait and estimate users' demography. However, the black-box nature of such deep learning models hinders the researchers from uncovering the reasons behind the model's predictions. Therefore, we propose leveraging deep learning and Layer-Wise Relevance Propagation (LRP) to identify the important variables that play a vital role in identifying the users' demography such as age and gender. To assess the efficacy of this approach we train a deep neural network model on a large sensor-based gait dataset consisting of 745 subjects to identify users' age and gender. Using LRP we identify the variables relevant for characterizing the gait patterns. Thus, we enable interpretation of non-linear ML models which are experts in identifying the users' demography based on inertial signals. We believe this approach can not only provide clinicians information about the gait parameters relevant to age and gender but also can be expanded to analyze and diagnose gait disorders.
Practitioners' Challenges and Perceptions of CI Build Failure Predictions at Atlassian

Continuous Integration (CI) build failures could significantly impact the software development process and teams, such as delaying the release of new features and reducing developers' productivity. In this work, we report on an empirical study that investigates CI build failures throughout product development at Atlassian. Our quantitative analysis found that the repository dimension is the key factor influencing CI build failures. In addition, our qualitative survey revealed that Atlassian developers perceive CI build failures as challenging issues in practice. Furthermore, we found that the CI build prediction can not only provide proactive insight into CI build failures but also facilitate the team's decision-making. Our study sheds light on the challenges and expectations involved in integrating CI build prediction tools into the Bitbucket environment, providing valuable insights for enhancing CI processes.