bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphological and Functional Outcomes >13 Years After Achilles Tendon Rupture Treated Operatively and Non-operatively
Authors: Willits Kevin , Birmingham Trevor , Spouge Alison , Bryant Dianne , Khan Michaela 
Published: July 2020

Objectives: In patients >13yrs after treatment for acute Achilles tendon rupture (AATR), 1) investigate side-to-side differences in MRI-defined morphological changes in the Achilles tendon and surrounding calf musculature, 2) investigate side-to-side differences in single-limb functional tasks, and 3) compare patients who received operative vs non-operative treatment. Methods: 28 patients (11 operative, 17 non-operative) from a previous randomized trial returned 15±1 years post-AATR for testing (age: 57±7 years; BMI: 30±5 kg/m2). Patients underwent bilateral 3T MRI (MAGNETOM Prisma, Siemens) including sagittal and axial T1 and T2-weighted turbo spin echo (TSE), axial T1-weighted inversion recovery, and sagittal T2-weighted 3D isotropic TSE sequences. The maximum anteroposterior Achilles tendon diameter (MAD) and cross-sectional area (CSA), distance from the MAD to the superior margin of the calcaneus, tendon length, gastrocnemius and soleus CSA, and calf circumference were measured using distance and area software tools (Figure 1; AGFA Healthcare). Functional measures included single-legged heel-rise repetitions and maximum vertical jump height. All outcomes were compared between limbs and between groups. Results: Overall, there were significant side-to-side differences in most MRI and functional measures, with the injured limb Achilles tendon typically wider and thicker (MAD often twice as large), calf musculature CSA smaller, number of heel raises lower, and vertical jump height lower (Table 1). The only differences between treatment groups was in MAD and the distance from the MAD to the superior margin of the calcaneus, with a greater side-to-side difference for patients treated operatively (Table 1). Conclusion: Substantial side-to-side differences in tendon diameter, thickness, muscle bulk and functional performance persist beyond a decade after treatment for AATR. There were no differences favoring operative treatment over non-operative treatment.
Oral Health Inequalities among Indigenous and Non-Indigenous Children
Authors: Haag D. , Schuch H. , Ha D. , Do L. , Jamieson L. 
Published: July 2020

Introduction: Our ability to address child oral health inequalities would be greatly facilitated by a more nuanced understanding of whether underlying disease experience or treatment opportunities account for a larger share of differences between social groups. This is particularly relevant in the context of population subgroups who are socially marginalized, such as Australia’s Indigenous population. The decayed, missing, and filled (dmf) surfaces index is at once a reflection of dental caries experience (d) and its management (m and f). Objectives: To 1) describe socioeconomic inequalities in dental caries experience and its management among Indigenous and non-Indigenous children and 2) compare these inequalities using absolute and relative measures. Methods: Data were from the Australian National Child Oral Health Study 2012–2014. Absolute and relative income inequalities were assessed for overall dmfs and its individual components (ds, ms, fs) using adjusted means and health disparity indices (Slope Index of Inequality [SII] and Relative Index of Inequality [RII]). Results: Mean dmfs among Indigenous children aged 5 to 10 y was 6.4 (95% confidence interval [CI], 5.4–7.4), ranging from 2.3 in the highest to 9.1 in the lowest income group. Mean dmfs among non-Indigenous children was 2.9 (95% CI, 2.8–3.1), ranging from 1.9 in the highest to 4.2 in the lowest income group. Age- and gender-adjusted social gradients for Indigenous children were evident across all dmfs components but were particularly notable for ds (SII = −4.6, RII = −1.7) and fs (SII = −3.2, RII = −1.5). The social gradients for non-Indigenous children were much lower in magnitude: ds (SII = −1.8, RII = −1.6) and fs (SII = −0.7, RII = −0.5). Conclusion: Our findings suggest that socioeconomic disadvantage may translate into both higher disease experience and increased use of dental services for both Indigenous and non-Indigenous groups, with the social gradients being much more amplified among Indigenous children. Knowledge Transfer Statement: The findings of this study demonstrate the magnitude of disparities in dental caries among children by population groups in Australia. Our results suggest that the relationship between socioeconomic disadvantage and poor oral health is more deleterious among Indigenous than non-Indigenous children. Tackling upstream determinants of health might not only affect population patterns of health and disease but also mitigate the overwhelming racial inequalities in oral health between Indigenous and non-Indigenous Australians.
TET family dioxygenases and the TET activator vitamin C in immune responses and cancer
Authors: Yue Xiaojing , Rao Anjana 
Published: July 2020

Abstract
Vitamin C serves as a cofactor for Fe(II) and 2-oxoglutarate–dependent dioxygenases including TET family enzymes, which catalyze the oxidation of 5-methylcytosine into 5-hydroxymethylcytosine and further oxidize methylcytosines. Loss-of-function mutations in epigenetic regulators such as TET genes are prevalent in hematopoietic malignancies. Vitamin C deficiency is frequently observed in cancer patients. In this review, we discuss the role of vitamin C and TET proteins in cancer, with a focus on hematopoietic malignancies, T regulatory cells, and other immune system cells.
MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes
Authors: Soltis Anthony R. , Dalgard Clifton L. , Pollard Harvey B. , Wilkerson Matthew D. 
Published: July 2020

AbstractBackgroundAnalysis of somatic mutations from tumor whole exomes has fueled discovery of novel cancer driver genes. However, ~ 98% of the genome is non-coding and includes regulatory elements whose normal cellular functions can be disrupted by mutation. Whole genome sequencing (WGS), on the other hand, allows for identification of non-coding somatic variation and expanded estimation of background mutation rates, yet fewer computational tools exist for specific interrogation of this space.ResultsWe present MutEnricher, a flexible toolset for investigating somatic mutation enrichment in both coding and non-coding genomic regions from WGS data. MutEnricher contains two distinct modules for these purposes that provide customizable options for calculating sample- and feature-specific background mutation rates. Additionally, both MutEnricher modules calculate feature-level and local, or “hotspot,” somatic mutation enrichment statistics.ConclusionsMutEnricher is a flexible software package for investigating somatic mutation enrichment that is implemented in Python, is freely available, can be efficiently parallelized, and is highly configurable to researcher's specific needs. MutEnricher is available online athttps://github.com/asoltis/MutEnricher.
IDSSIM: an lncRNA functional similarity calculation model based on an improved disease semantic similarity method
Authors: Fan Wenwen , Shang Junliang , Li Feng , Sun Yan , Yuan Shasha , Liu Jin-Xing 
Published: July 2020

Abstract
Background
It has been widely accepted that long non-coding RNAs (lncRNAs) play important roles in the development and progression of human diseases. Many association prediction models have been proposed for predicting lncRNA functions and identifying potential lncRNA-disease associations. Nevertheless, among them, little effort has been attempted to measure lncRNA functional similarity, which is an essential part of association prediction models.

Results
In this study, we presented an lncRNA functional similarity calculation model, IDSSIM for short, based on an improved disease semantic similarity method, highlight of which is the introduction of information content contribution factor into the semantic value calculation to take into account both the hierarchical structures of disease directed acyclic graphs and the disease specificities. IDSSIM and three state-of-the-art models, i.e., LNCSIM1, LNCSIM2, and ILNCSIM, were evaluated by applying their disease semantic similarity matrices and the lncRNA functional similarity matrices, as well as corresponding matrices of human lncRNA-disease associations coming from either lncRNADisease database or MNDR database, into an association prediction method WKNKN for lncRNA-disease association prediction. In addition, case studies of breast cancer and adenocarcinoma were also performed to validate the effectiveness of IDSSIM.

Conclusions
Results demonstrated that in terms of ROC curves and AUC values, IDSSIM is superior to compared models, and can improve accuracy of disease semantic similarity effectively, leading to increase the association prediction ability of the IDSSIM-WKNKN model; in terms of case studies, most of potential disease-associated lncRNAs predicted by IDSSIM can be confirmed by databases and literatures, implying that IDSSIM can serve as a promising tool for predicting lncRNA functions, identifying potential lncRNA-disease associations, and pre-screening candidate lncRNAs to perform biological experiments. The IDSSIM code, all experimental data and prediction results are available online at https://github.com/CDMB-lab/IDSSIM.
Ecomorphological divergence and habitat lability in the context of robust patterns of modularity in the cichlid feeding apparatus
Authors: Conith Andrew J. , Kidd Michael R. , Kocher Thomas D. , Albertson R. Craig 
Published: July 2020

AbstractBackgroundAdaptive radiations are characterized by extreme and/or iterative phenotypic divergence; however, such variation does not accumulate evenly across an organism. Instead, it is often partitioned into sub-units, or modules, which can differentially respond to selection. While it is recognized that changing the pattern of modularity or the strength of covariation (integration) can influence the range or rate of morphological evolution, the relationship between shape variation and covariation remains unclear. For example, it is possible that rapid phenotypic change requires concomitant changes to the underlying covariance structure. Alternatively, repeated shifts between phenotypic states may be facilitated by a conserved covariance structure. Distinguishing between these scenarios will contribute to a better understanding of the factors that shape biodiversity. Here, we explore these questions using a diverse Lake Malawi cichlid species complex,Tropheops,that appears to partition habitat by depth.ResultsWe construct a phylogeny ofTropheopspopulations and use 3D geometric morphometrics to assess the shape of four bones involved in feeding (mandible, pharyngeal jaw, maxilla, pre-maxilla) in populations that inhabit deep versus shallow habitats. We next test numerous modularity hypotheses to understand whether fish at different depths are characterized by conserved or divergent patterns of modularity. We further examine rates of morphological evolution and disparity between habitats and among modules. Finally, we raise a singleTropheopsspecies in environments mimicking deep or shallow habitats to discover whether plasticity can replicate the pattern of morphology, disparity, or modularity observed in natural populations.ConclusionsOur data support the hypothesis that conserved patterns of modularity permit the evolution of divergent morphologies and may facilitate the repeated transitions between habitats. In addition, we find the lab-reared populations replicate many trends in the natural populations, which suggests that plasticity may be an important force in initiating depth transitions, priming the feeding apparatus for evolutionary change.
MicroRNA-138 promotes neuroblastoma SH-SY5Y cell apoptosis by directly targeting DEK in Alzheimer’s disease cell model
Authors: Miao Jin , Jing Jin , Shao Yixiang , Sun Huaichang 
Published: July 2020

Abstract
Background
Alzheimer’s disease (AD) is a progressive neuro-degenerative disease with a major manifestation of dementia. MicroRNAs were reported to regulate the transcript expression in patients with Alzheimer’s disease (AD). In this study, we investigated the roles of miR-138, a brain-enriched miRNA, in the AD cell model.

Methods
The targets of miRNA-138 was predicted by bioinformatic analysis. The expression levels of DEK at both mRNA and protein levels were determined by qRT-PCR and Western blot, respectively. Luciferase assays were carried out to examine cell viabilities. Hoechst 33258 staining was used to detect cell apoptosis.

Results
Our results demonstrated that the expression levels of miR-138 were increased in AD model, and DEK was a target of miR-138. Overexpression of miR-138 in SH-SY5Y cells obviously down-regulated the expression of DEK in SH-SY5Y cells, resulting in the inactivation of AKT and increased expression levels of proapoptotic caspase-3. MiR-138 mediated-suppression of DEK increased the susceptibility of cell apoptosis.

Conclusions
MicroRNA-138 promotes cell apoptosis of SH-SY5Y by targeting DEK in SH-SY5Y AD cell model. The regulation of miR-138 may contribute to AD via down-regulation of the DEK/AKT pathway.
Early post-stress decrease in cardiac performance by impedance cardiography and its relationship to the severity and extent of ischemia by myocardial perfusion imaging
Authors: Goldkorn Ronen , Naimushin Alexey , Rozen Eli , Freimark Dov 
Published: July 2020

Abstract
Background
While single photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) is a well-established noninvasive procedure for the evaluation of patients with coronary artery disease (CAD), it is unable to detect the presence of, or underestimates the extent of CAD in certain patients. We aimed to show that a bio-impedance device can detect early post-stress changes in several hemodynamic parameters, thereby serving as a potential marker for the presence of significant ischemia.

Methods
Prospectively enrolled patients, referred to our Medical Center for clinically-indicated MPI, underwent testing using a Non-Invasive Cardiac System (NICaS) before and immediately after exercise. The differences between rest and stress hemodynamic parameters were compared with the severity and extent of myocardial ischemia by MPI. The study included 198 patients; mean age was 62 years, 26% were women, 54% had hypertension, and 29% diabetes mellitus. Of them, 188 patients had ≤10%, and 10 had > 10% of myocardial ischemia.

Results
In the first group, there was a significantly greater increase in post-exercise stroke index, stroke work index, cardiac index and cardiac power index (19.2, 29.1, 90.5 and 107%, respectively) compared with the second group (− 2.7, 3.8, 43.7 and 53.5%, respectively), as well as a significantly greater decrease in total peripheral resistance index (− 38.7% compared with − 16.3%), with corresponding p values of 0.015, 0.017, 0.040, 0.016, and < 0.001, respectively.

Conclusions
Our data suggest that immediate post-stress changes in several hemodynamic parameters, detected by the NICaS, can be used as an important adjunct to SPECT MPI for the early detection of myocardial ischemia.
A descriptive study of orthopaedic injuries due to parachute jumping in soldiers
Authors: Sahin Taner , Batın Sabri 
Published: July 2020

Abstract
Background
While parachute jumping, soldiers may suffer minor or life-threatening injuries in various parts of the body. Several trauma scoring systems assess the severity of such injuries. The primary goal of this study was to assess clinical characteristics and the severity of orthopaedic, musculoskeletal, and other injuries from military training-related parachute jumping using two trauma scoring systems (AIS and ISS). Our secondary goal was to assess whether there was an increase in injury rates with age.

Methods
In total, 185 military personnel between 19 and 51 years old who were injured as a result of daytime static parachute jumping during 44 months between January 2016 and August 2019 were included in the study. Demographic data; vital signs; the level of consciousness; the Glasgow Coma Scale; ISS trauma region classifications; anatomical injury sites; AIS and ISS scores; diagnoses; treatment methods; hospitalization status; and duration of hospital stay were examined descriptively.

Results
There were 184 male and one female participant. The most commonly injured body site was the foot (33.5%), and the most common diagnosis was soft tissue trauma (64.3%). The most commonly injured body site was the foot (33.5%), and the most common diagnosis was soft tissue trauma (64.3%). Regarding treatment methods, 51.4% received analgesic pills and cold pack application, 42.7% received a plaster splint, and 5.9% had orthopaedic surgery. The mean ISS score was 5.16 ± 3.92. The hospitalization rate was significantly higher for patients with a critical AIS score than those with a severe AIS score (p < 0.001).

Conclusions
The use of trauma scoring systems to assess injury severity among patients admitted to an ED due to a parachute jumping injury may facilitate treatment selection. We found that AIS and ISS were useful in determining injury severity. Therefore, we recommend the use of trauma scoring systems for assessing the injury severity and the therapeutic approach, and we advocate for the use of the 17 anatomical regions we used in this study. We also found that with increasing age, the severity of injury could increase.
Increasing prevalence of anticholinergic medication use in older people in England over 20 years: cognitive function and ageing study I and II
Authors: Grossi Carlota M. , Richardson Kathryn , Savva George M. , Fox Chris , Arthur Antony , Loke Yoon K. , Steel Nicholas , Brayne Carol , Matthews Fiona E. , Robinson Louise , Myint Phyo K. , Maidment Ian D. 
Published: July 2020

Abstract
Background
Anticholinergic medication use is linked with increased cognitive decline, dementia, falls and mortality, and their use should be limited in older people. Here we estimate the prevalence of anticholinergic use in England’s older population in 1991 and 2011, and describe changes in use by participant’s age, sex, cognition and disability.

Methods
We compared data from participants aged 65+ years from the Cognitive Function and Ageing Studies (CFAS I and II), collected during 1990–1993 (N = 7635) and 2008–2011 (N = 7762). We estimated the prevalence of potent anticholinergic use (Anticholinergic Cognitive Burden [ACB] score = 3) and average anticholinergic burden (sum of ACB scores), using inverse probability weights standardised to the 2011 UK population. These were stratified by age, sex, Mini-Mental State Examination score, and activities of daily living (ADL) or instrumental ADL (IADL) disability.

Results
Prevalence of potent anticholinergic use increased from 5.7% (95% Confidence Interval [CI] 5.2–6.3%) of the older population in 1990–93 to 9.9% (9.3–10.7%) in 2008–11, adjusted odds ratio of 1.90 (95% CI 1.67–2.16). People with clinically significant cognitive impairment (MMSE [Mini Mental State Examination] 21 or less) were the heaviest users of potent anticholinergics in CFAS II (16.5% [95% CI 12.0–22.3%]). Large increases in the prevalence of the use medication with ‘any’ anticholinergic activity were seen in older people with clinically significant cognitive impairment (53.3% in CFAS I to 71.5% in CFAS II).

Conclusions
Use of potent anticholinergic medications nearly doubled in England’s older population over 20 years with some of the greatest increases amongst those particularly vulnerable to anticholinergic side-effects.
Machine learning reveals that Mycobacterium tuberculosis genotypes and anatomic disease site impacts drug resistance and disease transmission among patients with proven extra-pulmonary tuberculosis
Authors: Sibandze Doctor B. , Magazi Beki T. , Malinga Lesibana A. , Maningi Nontuthuko E. , Shey Bong-Akee , Pasipanodya Jotam G. , Mbelle Nontombi N. 
Published: July 2020

Abstract
Background
There is a general dearth of information on extrapulmonary tuberculosis (EPTB). Here, we investigated Mycobacterium tuberculosis (Mtb) drug resistance and transmission patterns in EPTB patients treated in the Tshwane metropolitan area, in South Africa.

Methods
Consecutive Mtb culture-positive non-pulmonary samples from unique EPTB patients underwent mycobacterial genotyping and were assigned to phylogenetic lineages and transmission clusters based on spoligotypes. MTBDRplus assay was used to search mutations for isoniazid and rifampin resistance. Machine learning algorithms were used to identify clinically meaningful patterns in data. We computed odds ratio (OR), attributable risk (AR) and corresponding 95% confidence intervals (CI).

Results
Of the 70 isolates examined, the largest cluster comprised 25 (36%) Mtb strains that belonged to the East Asian lineage. East Asian lineage was significantly more likely to occur within chains of transmission when compared to the Euro-American and East-African Indian lineages: OR = 10.11 (95% CI: 1.56–116). Lymphadenitis, meningitis and cutaneous TB, were significantly more likely to be associated with drug resistance: OR = 12.69 (95% CI: 1.82–141.60) and AR = 0.25 (95% CI: 0.06–0.43) when compared with other EPTB sites, which suggests that poor rifampin penetration might be a contributing factor.

Conclusions
The majority of Mtb strains circulating in the Tshwane metropolis belongs to East Asian, Euro-American and East-African Indian lineages. Each of these are likely to be clustered, suggesting on-going EPTB transmission. Since 25% of the drug resistance was attributable to sanctuary EPTB sites notorious for poor rifampin penetration, we hypothesize that poor anti-tuberculosis drug dosing might have a role in the development of resistance.
Listeria spondylodiscitis: an uncommon etiology of a common condition; a case report
Authors: Al Ohaly Rand , Ranganath Nischal , Saffie Medina G. , Shroff Anjali 
Published: July 2020

Abstract
Background
Listeriosis is a severe food-borne infection caused by the Gram-positive rod, Listeria monocytogenes. Despite the low incidence (3–8 cases per million), Listeriosis has a case fatality rate of 20–30% as it occurs predominantly in immunocompromised individuals at extremes of age, diabetics and pregnant women. Listeriosis classically presents as a febrile gastroenteritis, isolated bacteremia, meningitis, or maternal-fetal infections. Focal bone and joint infection are rare and primarily involve orthopedic implant devices. Here, we present the first case of Listeria-associated spondylodiscitis.

Case presentation
A 79-year-old male presents with acute-on-chronic back pain in the absence of risk factors or exposures, aside from age. On radiological imaging, spondylodiscitis of L3-L4 was diagnosed. Subsequently, a CT-guided biopsy was performed to aid in confirming microbiological aetiology. Listeria monocytogenes was grown in culture and patient received appropriate antibacterial therapy.

Conclusion
The case highlights the utility of image-guided tissue sampling in aiding diagnosis and management in patients with vertebral osteomyelitis. It also encourages consideration of uncommon organisms such as Listeria as an etiology of vertebral osteomyelitis, even in the absence of prosthetic implants.