bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orthopaedic Gene Therapy
Authors: Evans Christopher H. , Ghivizzani Steve C. , Robbins Paul D. 
Published: August 2021

» Orthopaedics pioneered the expansion of gene therapy beyond its traditional scope of diseases that are caused by rare single-gene defects. Orthopaedic applications of gene therapy are most developed in the areas of arthritis and regenerative medicine, but several additional possibilities exist.» Invossa, an ex vivo gene therapeutic for osteoarthritis, was approved in South Korea in 2017, but its approval was retracted in 2019 and remains under appeal; a Phase-III clinical trial of Invossa has restarted in the U.S.» There are several additional clinical trials for osteoarthritis and rheumatoid arthritis that could lead to approved gene therapeutics for arthritis.» Bone-healing and cartilage repair are additional areas that are attracting considerable research; intervertebral disc degeneration and the healing of ligaments, tendons, and menisci are other applications of interest. Orthopaedic tumors, genetic diseases, and aseptic loosening are additional potential targets.» If successful, these endeavors will expand the scope of gene therapy from providing expensive medicines for a few patients to providing affordable medicines for many.
Comprehensive Studies of Formation Water for Achimov and Bazhenov Formations — Revitalizing Archived and Old Cores
Authors: Kazak Ekaterina Sergeevna , Kazak Andrey Vladimirovich 
Published: August 2021

Abstract
The sediments of Bazhenov (BF) and Achimov (ACh) formations have been studied for more than 50 years, and to date, a large amount of core material obtained during drilling at the stage of exploration is stored in the core stores of Russian industrial companies. The rise in the cost of the complex of geological exploration and the emergence of new research methods enabled studies of the old/dry core from previously drilled exploration wells. BF and ACh reservoir rocks have low permeability and initially low water saturation, and therefore, during storage, rock samples could partially retain pore water. To study its composition and quantitative content, we used the previously proposed integrated approach with proven effectiveness in fresh low-permeability BF rocks.
The studied materials include BF rock samples from 3 different fields stored for 2 years after sampling in the laboratory, and ACh rock samples from 12 fields, cored more than 10 years ago at the geologic exploration stage. The complex technique includes determining free and bound water contents by the evaporation method with isotopic analysis (δ18O and δD) of the released water. The modified water extraction method provides a range of pore water salinity, while the modified alcohol ammonium chloride method measures the cation exchange capacity (CEC). Auxilary methods include Rock-Eval pyrolysis to determine organic matter content, X-ray diffraction analysis (XRD) to assess the mineral composition of sediments. The verification of the results for the BF rock samples was carried out according to the data obtained for the new/fresh core, while for the ACh rock samples — according to the results of the direct chemical composition analysis of the formation water.
Despite the low permeability, we found that the BF and ACh rock samples during storage lost almost all (up to 90%) free water due to evaporation. At the same time, salts from formation water remained in the pore space, which made it possible to estimate the range of its NaCl salinity: 1.84–14.7 g/L for ACh rock samples and 4.49–20.19 g/L for BF rock samples. The obtained values set the lower limit of the possible pore water salinity of the studied ACh and BF rock samples. Moreover, the results match those from direct salinity measurements in the ACh depth intervals and the results of fresh BF core laboratory studies.
We showed that the old/dry BF and ACh core could be effectively used to assess the bound water content with subsequent determination of its genesis from isotopic composition data and CEC measurements. This opportunity relies on the high clay content in the studied BF and ACh rock samples.
The obtained results show the fundamental capability of informative laboratory studies of BF and ACh rock samples from public and private core storage facilities and give new life to archived and old/dry core.
Genomic Features and Comparative Genomic Analysis of Streptococcus sp. v1. nov., Isolated from an Endophthalmitis patient
Authors: Zheng Meiqin , Kang Yutong , Xu Yi , Xu Fangyi , Chen Yanjiong 
Published: August 2021

Abstract
Endophthalmitis is an acute inflammatory intraocular condition that can cause permanent vision loss. The treatment strategy and visual outcome partly depend on the identification of the pathogenic agents. In this study, metagenomic sequencing was conducted to investigate the microbiome of the vitreous of an endophthalmitis patient whose disease progressed rapidly and was accompanied by severe pain. Metagenomic sequencing data revealed that the vitreous sample was predominated by Streptococcus, with a low-diversity microbiome. The main antibiotic resistance gene (ARG) types included beta-lactam, macrolide-lincosamide-streptogramin, and multidrug resistance genes. Additionally, the metagenome-assembled genome sequence of Streptococcus sp. v1. nov. was isolated. The average nucleotide identities (ANI) and DNA–DNA hybridization (DDH) analysis between the genomes of Streptococcus sp. v1. nov and related species revealed that Streptococcus sp. v1. nov belongs to a new species. Pan/core genome analysis for Streptococcus sp. v1. nov. and tetra correlation search (TCS) top 25 hit strains revealed that most unique genes of Streptococcus sp. v1. nov. were linked to the ABC transporter system, which could indicate the unique virulence and pathogenic potential of Streptococcus sp. v1. nov. In addition, 7 virulence factors were identified in total, and most of them were classified as “offensive virulence factors”. The high pathogenicity of Streptococcus sp. v1. nov. could explain the patient's rapid disease progression. Our study first isolated an ocular pathogen with high virulence based on metagenomic sequencing and bioinformatics analysis, which has important reference value for revealing the composition and genome characteristics of pathogens in endophthalmitis patients in the future.
Site Response Analysis of S2 Soil Deposits Focusing on the Effects of Liquefaction and Pore-Pressure Dissipation on the Ground Surface Response Spectrum
Authors: Anthi Maria , GEROLYMOS NIKOS 
Published: August 2021

Abstract
A numerical algorithm for executing non-linear ground response analysis of layered sites is developed, capable of reproducing liquefaction phenomena, considering the simultaneous dissipation of the excess pore water pressure through soil grains. Τhe wave propagation algorithm is based on the plasticity constitutive model for sand Ta-Ger expressed in a one dimensional p-q space form, which exhibits remarkable versatility in representing complex patterns of sand cyclic behavior, such as stiffness decay and decrease in strength due to build-up of pore-water pressure. Its calibration is based on shear modulus reduction and damping curves for drained loading conditions and liquefaction resistance curves for undrained conditions. A detailed presentation of the numerical model formulation is provided, indicating the numerical approach of the wave propagation and consolidation differential equations. The recorded seismic ground response of the Port Island array from Kobe 1995 earthquake is used as a benchmark for testing the validity of model predictions. The model is finally applied to estimate the elastic response spectra at the surface of soil profiles with liquefiable layers (ground type S2) as per EC8:2004. The investigation study involves the ground response analysis of diverse soil profiles, all including a liquefiable zone, excited with a suite of earthquake motions at their base. The acceleration time histories were extracted from the PEER Ground Motion Database having characteristics compatible with the NGA-estimated response spectrum at the bedrock and with key seismological parameters such as the earthquake magnitude Mw and horizontal distance from the fault RJB. Two different methods are applied regarding the selection of base excitations: Amplitude scaled records (to match a target response spectrum) and spectral matched records. From the results an idealized response spectrum is deduced in terms of the design spectrum parameters S, η, ΤΒ and TC. It is shown that the idealized ground surface response spectrum is marginally sensitive to method of base excitation selection.
Biomarker-based treatment stratification in ADHD: An out-of-sample validation
Authors: Voetterl Helena , Wingen Guido van , Michelini Giorgia , Griffiths Kristi , Gordon Evian , deBeus Roger , Korgaonkar Mayuresh , Loo Sandra , Palmer Donna , Breteler Rien , Denys Damiaan , Arnold Eugene , du Jour Paul , Ruth Rosalinde van , Jansen Jeanine , Dijk Hanneke van , Arns Martijn 
Published: August 2021

Abstract
Attention-deficit/hyperactivity disorder (ADHD) is characterized by neurobiological heterogeneity, possibly explaining why not all patients benefit from a given treatment. As a means to select the right treatment (stratification), biomarkers may aid in personalizing treatment prescription, thereby increasing remission rates.The present study introduces a clinically interpretable and actionable, age- and sex-standardized biomarker based on individual alpha peak frequency (iAPF) assessed during resting-state electroencephalography (EEG). The biomarker was developed in a heterogeneous sample (N=4249), and stratifies patients with a higher iAPF to Methylphenidate (MPH; N=336) and those with a lower iAPF to Neurofeedback (NFB; N=136), resulting in a predicted gain in normalized remission of 17-30%. Blinded out-of-sample validation studies for MPH (N=58) and NFB (N=96) corroborated these findings, yielding a predicted gain in stratified normalized remission of 36% and 29%, respectively.These findings suggest that acknowledging neurobiological heterogeneity can inform stratification of patients to their individual best treatment and enhance remission rates.
The Impact of Different Phases of the El Niño-Southern Oscillation Phenomenon on Goiás State Rainfalls and Temperature Characteristics Across Three Decades
Authors: Matta David Henriques  da , Coelho Caio Augusto dos Santos , Santos Leydson Lara dos , Stone Luis Fernando , Heinemann Alexandre Bryan 
Published: August 2021

Abstract
Rainfall and temperature are the two key parameters of crop development. Studying the characteristics of these parameters under El Niño-Southern Oscillation (ENSO) conditions is important to better understand the impacts of the different phases of this phenomenon (El Niño, Neutral, and La Niña conditions) on agriculture. This study analyzes 32 years (1980–2011) of climatic data from 128 weather stations across Goiás State in Brazil to determine the behavior of temperature and rainfall time series over three periods (1980–1989; 1990–1999 and 2000–2011) under El Niño, Neutral, and La Niña conditions. The analysis revealed no major impacts of ENSO conditions on accumulated rainfall characteristics, a feature particularly marked in the most recent period (2000–2011). ENSO impacting temperature was identified but presented considerable variability across the periods investigated. These impacts were marked in the first two periods as for maximum temperature and increased from the first to the last period as for minimum temperature. These features were noticed in both analyses in the entire Goiás State and most of the investigated mega-regions, except for the East and Northeast mega-regions as for minimum temperature. There were increases in maximum temperature values throughout the rainfed season (October to March) for all ENSO conditions and investigated periods. Minimum temperature also increased across the three investigated periods, and this was marked in the beginning of the rainfed season (October) under El Niño and Neutral conditions.
Rheumatic heart disease knowledge and associated factors among nurses working in cardiac centers at public and private hospitals of Addis Ababa: cross sectional study
Authors: Techane Tesfaye , Legesse Bethlehem , Ayalew Yohannes , Hailu Aklil 
Published: August 2021

Abstract
Back ground: It is proposed that the biggest gap in control of rheumatic heart disease is in implementing of ineffective primary and secondary preventive measures. These measures are supposed to be well addressed by nurses. For prevention and proper management, nurses are expected to have full knowledge about rheumatic heart disease. Therefor the main objective of the study was to assess the level of nurse’s knowledge and factors behind regarding RHD in the current study. Method: Institution based cross sectional study was conducted on nurses working in cardiac centers of public and private hospitals at Addis Ababa from April 1 to 30, 2021. Total sample size is 163 selected by purposive sampling method. Data was entered in to Epi-data version 4.5 and exported to SPSS version 25.0 and was checked for missing values. Data was cleaned. Descriptive statistics such as frequency, mean and percentages were calculated, described and displayed in tables, graphs and charts. Binary logistic regression was done to see the crude significant relation of each independent variable with nurse’s good knowledge score. Significant factors were identified based on multivariate logistics regression in 95% confidence level at P-value less than 0.05. Result: In the present study about 154 participants were participated. The mean correct answer response of the nurses for knowledge of RHD questions is 12.2 ± 5.2. Only 48.7% of the nurses have good knowledge towards RHD. Being male in gender, having history of sore throat, taking formal education in university or collage, taking in-service training on RHD, having higher wok experience, have found significantly associated with higher odds of nurses’ good knowledge towards RHD. Conclusion and recommendation: regular training regarding RHD management should be given to nurses who are working in cardiac centers. Rheumatic heart disease early treatment and prevention should be incorporated and reinforced in to nursing and other health related professions curriculums.
Improving CNN-Based Pest Recognition with a Post-Hoc Explanation of XAI
Authors: Chen Ching-Ju , Chen Ling-Wei , Yang Chun-Hao , Huang Ya-Yu , Huang Yueh-Min 
Published: August 2021

Abstract
Deep learning is currently quite prevalent and is often used in image classification or object detection. This article adds emerging research on the use of explainable AI (XAI) in Tessaratoma papillosa pest identification and investigates the connotation and importance of XAI, interpretability classification standards, and neural network interpretation methods and compares the quality of interpretations between different approaches and various trade-offs. The experimental results include the data processing in the research, the establishment of training models, a comparison of the results and feature visualization methods, and the consequences of improving the training models. First, we analyzed the data processing methods of the dataset, trained the VGG16 model, and finally added a visual interpretation method to the model to visualize and explain the model identification results. The experimental results indicated that the best visual discrimination effect was obtained through eXplanation with Ranked Area Integrals (XRAI). In this study, XAI was used to obtain the factors contributing to incorrect predictions based on post-hoc explanations. Based on the inferenced result, we proposed an adjustment method for improving the model accuracy as a basis for future research to subsequently adjust and improve the model. It is hoped that the experimental results of this study can provide researchers in artificial intelligence useful information so that they can use XAI to acquire appropriate interpretations to correct recognition accuracy and drive the development of XAI.
Factors Affecting Knowledge Regarding Unmet Need On Fertile Aged Women in Indonesia: Evaluation of 2012 and 2017 IDHS
Authors: Harzif Achmad Kemal , Maidarti Mila , Handayaning Fransisca Novi , Andyra Azizah Fitriayu 
Published: August 2021

Abstract
Background
The Family Planning (FP/KB) Program is a national method of controlling population growth rates while improving maternal and child health. Indonesia, as one of the largest countries, has abysmally low contraceptive coverage. One of its main issues is unmet contraceptive needs. This study aims to determine the factors that influence women's unmet need of childbearing age (WCA) in Indonesia.
Method:
An unpaired comparative analytic study with a cross-sectional method was conducted on secondary data obtained from 2012 and 2017 Indonesia Demographic and Health Survey (IDHS). The subjects in this study were all women of childbearing age (15–49 years). Subjects with incomplete data were excluded from the study. Unmet need was defined as WCA who did not use contraception but decline to have more children or wanted to delay their pregnancies. Chi-square analysis was performed on categorical data and Mann-Whitney U analysis on numerical data.
Result
A total of 45,607 WCA in the 2012 IDHS data and 29,627 WCA in the 2017 IDHS data were included in the study. In the 2012 IDHS data, factors influencing unmet needs were age (p = 0.023) and parity (p < 0.0001). In the 2017 IDHS data, factors influencing unmet needs were the residential area (p = 0.003), level of education (p = 0.008), level of spouse’s education (p < 0.0001), employment status (p = 0.03), possession of electricity (p = 0.001), and possession of television (p = 0.01)
Conclusion
Factors affecting unmet needs are age, parity, residential area, level of education, level of spouse's education, employment status, possession of television, and possession of electricity. There were no recurring factors on 2012 and 2017 IDHS data.
Clinicians’ Perceptions of The Health Status of Formerly Detained Immigrants
Authors: Hampton Kathryn , Mishori Ranit , Griffin Marsha , Hillier Claire , Pirrotta Elizabeth , Wang Nancy E. 
Published: August 2021

Abstract
Background

In the past decade, the U.S. immigration detention system regularly detained more than 30,000 people; in 2019 prior to the pandemic, the detention population exceeded 52,000 people. Inhumane detention conditions have been documented by internal government watchdogs, news media and human rights groups, finding over-crowding, poor hygiene and sanitation and poor and delayed medical care, as well as verbal, physical and sexual abuse.
Methods

This study surveyed health professionals across the United States who had provided care for immigrants who were recently released from immigration detention to assess clinician perceptions about the adverse health impact of immigration detention on migrant populations based on real-life clinical encounters. There were 150 survey responses, of which 85 clinicians observed medical conditions attributed to detention.
Results

These 85 clinicians reported seeing a combined 1300 patients with a medical issue related to their time in detention, including patients with delayed access to medical care or medicine in detention, patients with new or acute health conditions including infection and injury attributed to detention and patients with worsened chronic conditions or special needs conditions. Clinicians also provided details regarding sentinel cases, categorized into the following themes: Pregnant women, Children, Mentally Ill, COVID-19, and Other serious health issue.
Conclusions

This is the first survey, to our knowledge, of health care professionals treating individuals upon release from detention. Due to the lack of transparency by federal entities and limited access to detainees, this survey serves as a source of credible information about conditions experienced within immigration detention facilities and is a means of corroborating immigrant testimonials and media reports. These findings can help inform policy discussions regarding systematic changes to the delivery of healthcare in detention, quality assurance and transparent reporting.
Dogs (Canis Familiaris) Underestimate The Quantity of Connected Items: First Demonstration of Susceptibility To The Connectedness Illusion in Non-Human Animals
Authors: Lõoke Miina , Marinelli Lieta , Agrillo Christian , Guérineau Cécile , Mongillo Paolo 
Published: August 2021

Abstract
In humans, numerical estimation is affected by perceptual biases, such as those originating from the spatial arrangement of elements. Different animal species can also make relative quantity judgements. This includes dogs, who have been proposed as a good model for comparative neuroscience. However, dogs do not show the same perceptual biases observed in humans. Thus, the exact perceptual/cognitive mechanisms underlying quantity estimations in dogs and their degree of similarity with humans are still a matter of debate. Here we explored whether dogs are susceptible to the connectedness illusion, an illusion based on the tendency to underestimate the quantity of interconnected items. Dogs were first trained to choose the larger of two food arrays. Then, they were presented with two arrays containing the same quantity of food, of which one had items interconnected by lines. Dogs significantly selected the array with unconnected items, suggesting that, like in humans, connectedness determines underestimation biases, possibly disrupting the perceptual system’s ability to segment the display into discrete objects. The similarity in dogs’ and humans’ susceptibility to the connectedness, but not to other numerical illusions, suggests that different mechanisms are involved in the estimation of quantity of stimuli with different characteristics.
Differential Analysis of RNA Structure Probing Experiments at Nucleotide Resolution: Uncovering Regulatory Functions of RNA Structure
Authors: Yu Bo , Li Pan , Zhang Qiangfeng , Hou Lin 
Published: August 2021

Abstract
RNAs perform their function by forming specific structures, which can change across cellular conditions. Structure probing experiments combined with next generation sequencing technology have enabled transcriptome-wide analysis of RNA secondary structure in various cellular conditions. Differential analysis of structure probing data in different conditions can reveal the RNA structurally variable regions (SVRs), which is important for understanding RNA functions. Here, we propose DiffScan, a computational framework for normalization and differential analysis of structure probing data in high resolution. DiffScan preprocesses structure probing datasets to remove systematic bias, and then scans the transcripts to identify SVRs and adaptively determines their lengths and locations. The proposed approach is compatible with most structure probing platforms (e.g., icSHAPE, DMS-seq). When evaluated with simulated and benchmark datasets, DiffScan identifies structurally variable regions at nucleotide resolution, with substantial improvement in accuracy compared with existing SVR detection methods. Moreover, the improvement is robust when tested in multiple structure probing platforms. Application of DiffScan in a dataset of multi-subcellular RNA structurome identified multiple regions that form different structures in nucleus and cytoplasm, linking RNA structural variation to regulation of mRNAs encoding mitochondria-associated proteins. This work provides an effective tool for differential analysis of RNA secondary structure, reinforcing the power of structure probing experiments in deciphering the dynamic RNA structurome.