bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does capsular closure influence patient-reported outcomes in hip arthroscopy for femoroacetabular impingement and labral tear?
Authors: Atzmon Ran , Sharfman Zachary T , Haviv Barak , Frankl Michal , Rotem Gilad , Amar Eyal , Drexler Michael , Rath Ehud 
Published: July 2019

Abstract
Capsulotomy is necessary to facilitate instrument manoeuvrability within the joint capsule in many arthroscopic hip surgical procedures. In cases where a clear indication for capsular closure does not exist, surgeon’s preference and experience often determines capsular management. The purpose of this study was to assess the influence of capsular closure on clinical outcome scores and satisfaction in patients who underwent hip arthroscopy surgery for femoroacetabular impingement (FAI) and labral tear. Data were prospectively collected and retrospectively analysed for hip arthroscopy surgeries with a minimum 2 years follow-up. Patients with developmental dysplasia of the hip, previous back or hip surgeries, and degenerative changes to this hip and secondary gains were excluded. Demographic data, intraoperative findings and patient-reported outcome scores were recorded, including the Modified Harris Hip Score (MHHS) and Hip Outcome Score (HOS). A total of 29 and 35 patients were included in the non-closure and closure groups, respectively. The mean follow-up time was over 3 years for both groups. The mean pre-operative and post-operative HOS scores and MHHS scores did not significantly differ between groups (pre-operative HOS: 65.6 and 66.3, P = 0.898; post-operative HOS: 85.4 and 87.2, P = 0.718; pre-operative MHHS: 63.2 and 58.4, P = 0.223; post-operative MHHS: 85.7 and 88.7, P = 0.510). Overall patient satisfaction did not differ significantly between groups (non-closure 86.3%, closure group 88.6%; P = 0.672). Capsular closure did not significantly influence satisfaction or clinical outcome scores in patients who underwent arthroscopic hip surgery for FAI or labral tear.
Psychopathology and Truth: A Defense of Realism
Authors: Eronen Markus I 
Published: July 2019

AbstractRecently Kenneth Kendler and Peter Zachar have raised doubts about the correspondence theory of truth and scientific realism in psychopathology. They argue that coherentist or pragmatist approaches to truth are better suited for understanding the reality of psychiatric disorders. In this article, I show that rejecting realism based on the correspondence theory is deeply problematic: It makes psychopathology categorically different from other sciences, and results in an implausible view of scientific discovery and progress. As an alternative, I suggest a robustness-based approach that can accommodate the significance of coherence and pragmatic factors without rejecting scientific realism and the correspondence theory of truth.
Semiclassical perturbation Stark shifts of singly charged argon spectral lines
Authors: Hamdi Rafik , Ben Nessib Nabil , Sahal-Bréchot Sylvie , Dimitrijević Milan S 
Published: July 2019

AbstractUsing semiclassical perturbation approach in impact approximation, Stark shifts for singly charged argon (Ar ii) spectral lines have been calculated. Energy levels and oscillator strengths needed for this calculation were determined using Hartree–Fock method with relativistic correction (HFR). We compare our results with experimental values for 100 spectral lines. We also present results as a function of temperature for 161 spectral lines for collisions with electrons, protons, singly charged helium and singly charged argon. This work extends our previous one.
ExoMol line list – XXXIV. A rovibrational line list for phosphinidene (PH) in its $X\, {}^3\Sigma ^-$ and $a\, {}^1\Delta$ electronic states
Authors: Langleben Jonathan , Tennyson Jonathan , Yurchenko Sergei N , Bernath Peter 
Published: July 2019

ABSTRACTA rovibronic line list for the ground (X 3Σ−) and first excited (a 1Δ) states of phosphinidene, 31PH, is computed. The line list is designed for studies of exoplanetary and cool stellar atmospheres with temperatures up to 4000 K. A combination of empirical and ab initio data is used to produce the line list: potential energy curves (PECs) are fitted using experimental transition frequencies; these transitions are reproduced with a root mean square error of 0.01 cm−1. The nuclear Schrödinger equation is solved using these PECs plus Born–Oppenheimer and spin splitting correction terms. Line intensities and Einstein A coefficients are computed using ab initio dipole moment curves for X–X and a–a transitions. The resulting LaTY line list, which contains 65 055 transitions for 2528 rovibronic states up to 24 500 cm −1 and J = 80, is used to simulate spectra in emission and absorption for a range of temperatures. The line list is made available in electronic form at the CDS and ExoMol data bases.
Misdiagnosis of Lyme Disease With Unnecessary Antimicrobial Treatment Characterizes Patients Referred to an Academic Infectious Diseases Clinic
Authors: Kobayashi Takaaki , Higgins Yvonne , Samuels Roger , Moaven Aurasch , Sanyal Abanti , Yenokyan Gayane , Lantos Paul M , Melia Michael T , Auwaerter Paul G 
Published: July 2019

Abstract

Background
Although Lyme disease is the most common vector-borne infection in the United States, diagnostic accuracy within community settings is not well characterized.

Methods
A retrospective observational cohort study of patients referred to an academic center with a presumed diagnosis or concern for Lyme disease between 2000 and 2013 was performed to analyze diagnoses and treatments. Characteristics of those with Lyme disease and those misdiagnosed as having Lyme disease were compared.

Results
Of 1261 patients, 911 (72.2%) did not have Lyme disease, 184 (14.6%) had active or recent Lyme disease, 150 (11.9%) had a remote history of Lyme disease, and 16 (1.3%) were identified as having possible Lyme disease. Patients without current Lyme disease were more likely to be female (odds ratio [OR], 1.56; 95% confidence interval [CI], 1.08–2.45), to have had symptoms for &gt;3 months (OR, 8.78; 95% CI, 5.87–13.1), to have higher symptom counts (OR per additional symptom, 1.08; 95% CI, 1.02–1.13), to have had more Lyme-related laboratory testing (OR per additional laboratory test, 1.17; 95% CI, 1.03–1.32), and to have been diagnosed with what were regarded as coinfections (OR, 3.13; 95% CI, 1.14–8.57). Of the 911 patients without Lyme disease, 764 (83.9%) had received antimicrobials to treat Lyme disease or their coinfections. The percentage of patients established to have Lyme disease was lower than in earlier studies of referred populations.

Conclusions
Among patients referred to an academic Infectious Diseases practice for Lyme disease, incorrect diagnoses and unnecessary antibiotic treatment were common, both for Lyme disease and for coinfections.
Efficacy of Superior Hypogastric Plexus Neurolysis for the Treatment of Cancer-Related Pelvic Pain
Authors: Hou Saiyun , Novy Diane , Felice Francis , Koyyalagunta Dhanalakshmi 
Published: July 2019

AbstractObjectiveCancer-related abdominal and pelvic pain syndromes can be debilitating and difficult to treat. The objective of this study was to evaluate the efficacy of superior hypogastric plexus blockade or neurolysis (SHPN) for the treatment of cancer-related pelvic pain.DesignRetrospective study.SettingMD Anderson Cancer Center, Houston, Texas.MethodsWe enrolled 46 patients with cancer-related pelvic pain who underwent SHPN. A numeric rating scale (NRS) was used for pain intensity, and symptom burden was evaluated using the Edmonton Symptom Assessment System at baseline, visit 1 (within one month), and visit 2 (within one to six months).ResultsForty-six patients who received SHPN showed a significant reduction in pain score from 6.9 to 5.6 at visit 1 (P = 0.01). Thirty of the 46 patients continued to complete visit 2 follow-up, and the NRS score was consistently lower at 4.5 at visit 2 (P &lt; 0.0001), with anxiety and appetite improved significantly. There was no significant change in the morphine equivalent dose at visits 1 and 2. The efficacy of the block was not influenced by patients’ age, gender, type of cancer, cancer stage, regimen of chemotherapy and/or radiation therapy, diagnostic block, approach or laterality of procedure, or type or amount of neurolytic agent. Nonsmokers with high baseline pain scores were more likely to have improved treatment outcomes from SHPN at short-term follow-up. Adverse effects with SHPN were mild and well tolerated.ConclusionsSHPN was an effective and relatively safe procedure for pain associated with pelvic malignancies. There is a need for larger prospective trials.
Association of gout medications and risk of cataract: a population-based case–control study
Authors: Li Y-J , Perng W-T , Tseng K-Y , Wang Y-H , Wei J C-C 
Published: July 2019

Abstract

Background
The relationship between gout medication use and cataract development is controversial. Moreover, limited clinical studies have evaluated this relationship.

Aim
To assess the effects of colchicine, allopurinol and benzbromarone on the risk of cataract in patients with gout.

Design
Population-based nested case–control study.

Methods
We enrolled 7900 patients who had received a new diagnosis of cataract >3 years after gout diagnosis into the study group and 33 475 patients who did not receive a diagnosis of cataract into the control group by matching for age, sex and the year of gout diagnosis at a ratio of 1:1. We used World Health Organization’s defined daily dose (DDD) as a measure to assess the dosage of colchicine, allopurinol and benzbromarone exposure. Logistic regression was used to estimate crude and adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for the risk of cataract.

Results
The risk of cataract significantly increased in patients who received colchicine at a cumulative DDD of ≥66.5 (OR = 1.17, 95% CI = 1.01–1.36, P = 0.041). In the age-stratified analysis, patients with gout aged >60 years had a higher risk of cataract (OR = 1.27, 95% CI = 1.06–1.53, P = 0.011) than did patients aged <60 years. Allopurinol and benzbromarone had no association with cataract.

Conclusions
In this population-based nested case–control study, we observed that colchicine use increased the risk of cataract in patients with gout, especially in those aged >60 years who received colchicine at a cumulative DDD of >66.5.
Different factors underlie recurrent and de novo organ involvement in immunoglobulin G4–related disease
Authors: Mizushima Ichiro , Tsuge Syunsuke , Fujisawa Yuhei , Hara Satoshi , Suzuki Fae , Ito Kiyoaki , Fujii Hiroshi , Yamada Kazunori , Kawano Mitsuhiro 
Published: July 2019

Abstract

Objectives
In IgG4-related disease (IgG4-RD), relapse including recurrent organ involvement (ROI) and de novo organ involvement (DNOI) occurs frequently during the clinical course. This study aimed to clarify the differences between the risk factors underlying ROI and DNOI in IgG4-RD.

Methods
We retrospectively investigated factors related to ROI and DNOI in 86 IgG4-RD patients. For assessment of factors related to ROI and DNOI, we performed uni- and multivariate Cox regression analyses. On stepwise multivariate analysis, we applied the variables with P < 0.1 in the univariate analysis and the predictors of relapse suggested in past reports.

Results
During the mean follow-up period of 63.1 months, ROI was detected at 1.0–120 months after diagnosis in 20 patients, 4 of whom were not receiving glucocorticoid (GC) at the time of ROI. In contrast, DNOI was detected at 5.0–120 months after diagnosis in 15 patients, 8 of whom were not receiving GC at the time of DNOI. In the multivariate analysis, blood eosinophil counts at diagnosis [per 100/μl; hazard ratio (HR) 1.072 (95% CI 1.018, 1.129)] and continuation of GC [vs discontinuation or observation without GC; HR 0.245 (95% CI 0.076, 0.793)] had a significant impact on the time to DNOI, whereas age [HR 0.942 (95% CI 0.899, 0.986)] and ANA positivity [vs negativity; HR 6.632 (95% CI 1.892, 23.255)] had a significant impact on the time to ROI.

Conclusion
The present study suggests that the risk factors of ROI and DNOI are different in IgG4-RD, highlighting the need for different preventative strategies.
Is Routine Monitoring for Hypoglycemia Required in Intramural Asymptomatic Infant of Diabetic Mother? An Audit in a Tertiary Care Hospital
Authors: Khandare Jayant , DS Madhusudhan , Ananthan Anitha , Nanavati Ruchi 
Published: July 2019

Abstract

Aims
This retrospective audit aimed to analyze whether routine frequent monitoring for hypoglycemia is required in asymptomatic infant of diabetic mother born in tertiary care hospital.

Methods
The study analyzed the blood sugar level of 196 infants of diabetic mothers.

Results
The overall incidence of hypoglycemia from 196 study participants was 9.18% (N = 18). The incidence of hypoglycemia at 2 h of life was maximum (83.33%) and it was significant when compared to 3, 6, 9 and 12 h (p &lt; 0.0001). Blood glucose levels were significantly more at 6 (p = 0.0002)), 9 (p = 0.0001) and 12 h (p = 0.0001) when compared to glucose level at 2 h except at 3 h of life (p = 0.062). Similarly blood glucose at 9 (p = 0.0001) and 12 h of life (p = 0.0002) were significantly more than at 3 h of life. Blood glucose at 9 h was significantly more than at 6 h of life (0.032) and at 12 hours of life (p = 0.0237) was significantly higher than at 6 h of life.

Conclusion
The frequent blood glucose monitoring for hypoglycemia in infant of diabetic mother as per American Academy of Pediatrics may be reduced as per the findings in our study. However, this needs to be confirmed by a properly designed observational study/adequately powered randomized controlled trial.
Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis
Authors: Benítez-Burraco Antonio , Chekalin Evgeny , Bruskin Sergey , Morozova Irina 
Published: July 2019

AbstractHuman evolution resulted from changes in our biology, behavior, and culture. One source of these changes has been hypothesized to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times. In this paper we compare whole-genome data between Late Neolithic/Bronze Age individuals and modern Europeans and show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups. We hypothesize how these changes might account for the increased features of self-domestication in modern humans and ultimately, for subtle recent changes in human cognition and behavior, including language.
Deep learning detects virus presence in cancer histology
Authors: Kather Jakob Nikolas , Schulte Jefree , Grabsch Heike I. , Loeffler Chiara , Muti Hannah , Dolezal James , Srisuwananukorn Andrew , Agrawal Nishant , Kochanny Sara , Stillfried Saskia von , Boor Peter , Yoshikawa Takaki , Jaeger Dirk , Trautwein Christian , Bankhead Peter , Cipriani Nicole A. , Luedde Tom , Pearson Alexander T. 
Published: July 2019

AbstractOncogenic viruses like human papilloma virus (HPV) or Epstein Barr virus (EBV) are a major cause of human cancer. Viral oncogenesis has a direct impact on treatment decisions because virus-associated tumors can demand a lower intensity of chemotherapy and radiation or can be more susceptible to immune check-point inhibition. However, molecular tests for HPV and EBV are not ubiquitously available.We hypothesized that the histopathological features of virus-driven and non-virus driven cancers are sufficiently different to be detectable by artificial intelligence (AI) through deep learning-based analysis of images from routine hematoxylin and eosin (HE) stained slides. We show that deep transfer learning can predict presence of HPV in head and neck cancer with a patient-level 3-fold cross validated area-under-the-curve (AUC) of 0.89 [0.82; 0.94]. The same workflow was used for Epstein-Barr virus (EBV) driven gastric cancer achieving a cross-validated AUC of 0.80 [0.70; 0.92] and a similar performance in external validation sets. Reverse-engineering our deep neural networks, we show that the key morphological features can be made understandable to humans.This workflow could enable a fast and low-cost method to identify virus-induced cancer in clinical trials or clinical routine. At the same time, our approach for feature visualization allows pathologists to look into the black box of deep learning, enabling them to check the plausibility of computer-based image classification.
Female-specific and dosage selections restore genes through transpositions onto the degenerated songbird W chromosomes
Authors: Xu Luohao , Zhou Qi 
Published: July 2019

AbstractSex chromosomes are usually suppressed for homologous recombination, which leads to the loss of functional genes on the Y or W chromosomes. It remains unclear how species like birds with a ZW sex system cope with the consequential gene expression imbalance, usually in the absence of global dosage compensation mechanism. Here we tackle this conundrum by reporting 14 genes recently transposed from the Z to the W chromosomes of three songbird lineages, after analyzing a total of 12 songbird species’ genomes. These transpositions are estimated to have occurred within 9 million years. Besides the expected signatures of functional degeneration in some genes on the non-recombining W chromosomes, the other retained genes after transposition are enriched for haploinsufficient genes or housekeeping genes. Several genes show biased expression in ovaries of birds or lizard, or function in female germ cells. These results, together with the reported X-to-Y transpositions provide direct evidence that sex-specific and dosage selections may have recurrently driven the restoration of genes on the Y or W chromosomes, and suggest their evolutionary processes are more dynamic than simply becoming completely degenerated.
Integrative Analysis of Axolotl Gene Expression Data From Regenerative and Wound Healing Limb Tissues
Authors: Sibai Mustafa , Parlayan Cüneyd , Tuğlu Pelin , Öztürk Gürkan , Demircan Turan 
Published: July 2019

ABSTRACTAxolotl (Ambystoma mexicanum) is a urodele amphibian endowed with remarkable regenerative capacities manifested in scarless wound healing and full restoration of amputated limbs. Several regenerative cues of the axolotl limb were successfully unraveled due to the advent of high-throughput technologies and their employment in tackling research questions on several OMICS levels. The field of regenerative biology and medicine has therefore utilized the axolotl as a major and powerful experimental model. Studies which have previously unraveled differentially expressed (DE) genes en masse in different phases of the axolotl limb regeneration have primarily used microarrays and RNA-Seq technologies. However, as different labs are conducting such experiments, sufficient consistency may be lacking due to statistical limitations arising from limited number of sample replicates as well as possible differences in study designs. This study, therefore, aims to bridge such gaps by performing an integrative analysis of publicly available microarray and RNA-Seq data from axolotl limb samples having comparable study designs. Three biological groups were conceived for the analysis; homeostatic tissues (control group), from amputation/injury timepoint up to around 50 hours post amputation (wound healing group), and from 50 hours to 28 days post amputation/injury (regenerative group). Integrative analysis was separately carried out on the selected microarray and RNA-Seq data from axolotl limb samples using the “merging” method. Differential expression analysis was separately implemented on the processed data from both technologies using the R/Bioconductor “limma” package. A total of 1254 genes (adjusted P < 0.01) were found DE in regenerative samples compared to the control, out of which 351 showed magnitudes of Log Fold Changes (LogFC) > 1 and were identified as the top DE genes from data of both technologies. Downstream analyses illustrated consistent correlations of the logFCs of DE genes distributed among the biological comparisons, within and between both technologies. Gene ontology annotations demonstrated concordance with the literature on the biological process involved in the axolotl limb regeneration. qPCR analysis validated the observed gene expression level differences between regenerative and control samples for a set of five genes. Future studies may benefit from the utilized concept and approach for enhanced statistical power and robust discovery of biomarkers of regeneration.
Perceived direction of deformation flow
Authors: Kawabe Takahiro 
Published: July 2019

AbstractIn everyday circumstances, human observers can easily discriminate the direction of transparent liquid flow. However, the mechanism of direction discrimination is not so straightforward. The present study focused on the flow of image deformation, which is closely related to the flow of transparent liquid in the natural world. To determine what image information is important in discriminating the direction of deformation flow, a natural image in a stimulus clip was deformed by using a deformation vector map that translated leftward or rightward. The task of the observers was to judge whether the transparent liquid in the clip flowed leftward or rightward. Manipulating the amplitude of deformation, we found that the discrimination performance improved with the amplitude. Interestingly, the observers’ performance was high overall only when shearing deformation was applied to the stimuli, while the observers reported an opposite-motion direction when only compressive deformation was applied. We computationally analyzed motion statistics of stimuli and found that the combination of mean and skewness of horizontal motion vectors reliably predicted the performance. The results indicate that human observers use global motion directions in order to determine the direction of deformation flow.
Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae family
Authors: Rajarammohan Sivasubramanian , Paritosh Kumar , Pental Deepak , Kaur Jagreet 
Published: July 2019

AbstractAlternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and A. alternata are known to cause secondary infections in the A. brassicae-infected Brassicas. The genome architecture, pathogenicity factors, and determinants of host-specificity of A. brassicae are unknown. In this study, we annotated and characterised the recently announced genome assembly of A. brassicae and compared it with other Alternaria spp. to gain insights into its pathogenic lifestyle. Additionally, we sequenced the genomes of two A. alternata isolates that were co-infecting B. juncea. Genome alignments within the Alternaria spp. revealed high levels of synteny between most chromosomes with some intrachromosomal rearrangements. We show for the first time that the genome of A. brassicae, a large-spored Alternaria species, contains a dispensable chromosome. We identified 460 A. brassicae-specific genes, which included many secreted proteins and effectors. Furthermore, we have identified the gene clusters responsible for the production of Destruxin-B, a known pathogenicity factor of A. brassicae. The study provides a perspective into the unique and shared repertoire of genes within the Alternaria genus and identifies genes that could be contributing to the pathogenic lifestyle of A. brassicae.