Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of spermatogenesis by a local functional axis in the testis: role of the basement membrane–derived noncollagenous 1 domain peptide

Spermatogenesis takes place in the epithelium of the seminiferous tubules of the testes, producing millions of spermatozoa per day in an adult male in rodents and humans. Thus, multiple cellular events that are regulated by an array of signaling molecules and pathways are tightly coordinated to support spermatogenesis. Here, we report findings of a local regulatory axis between the basement membrane (BM), the blood‐testis barrier (BTB), and the apical ectoplasmic specialization (apical ES; a testis‐specific, actin‐rich adherens junction at the Sertoli cell–spermatid interface) to coordinate cellular events across the seminiferous epithelium during the epithelial cycle. In short, a biologically active fragment, noncollagenous 1 (NC1) domain that is derived from collagen chains in the BM, was found to modulate cell junction dynamics at the BTB and apical ES. NC1 domain from the collagen α3(IV) chain was cloned into a mammalian expression vector, pCI‐neo, with and without a collagen signal peptide. We also prepared a specific Ab against the purified recombinant NC1 domain peptide. These reagents were used to examine whether overexpression of NC1 domain with high transfection efficacy would perturb spermatogenesis, in particular, spermatid adhesion (i.e., inducing apical ES degeneration) and BTB function (i.e., basal ES and tight junction disruption, making the barrier leaky), in the testis in vivo. We report our findings that NC1 domain derived from collagen α3(IV) chain—a major structural component of the BM—was capable of inducing BTB remodeling, making the BTB leaky in studies in vivo. Furthermore, NC1 domain peptide was transported across the epithelium via a microtubule‐dependent mechanism and is capable of inducing apical ES degeneration, which leads to germ cell exfoliation from the seminiferous epithelium. Of more importance, we show that NC1 domain peptide exerted its regulatory effect by disorganizing actin microfilaments and microtubules in Sertoli cells so that they failed to support cell adhesion and transport of germ cells and organelles (e.g., residual bodies, phagosomes) across the seminiferous epithelium. This local regulatory axis between the BM, BTB, and the apical ES thus coordinates cellular events that take place across the seminiferous epithelium during the epithelial cycle of spermatogenesis. —Chen, H. , Mruk, D. D. , Lee, W. M. , Cheng, C. Y. Regulation of spermatogenesis by a local functional axis in the testis: role of the basement membrane–derived noncollagenous 1 domain peptide. FASEB J. 31, 3587–3607 (2017). www.fasebj. org
Endogenous stages of a ‘chick embryo-adapted’ strain of Eimeria tenella

A strain of E. tenella which had been passaged serially in 42 batches of chick embryos appeared to have lost its ability to produce the characteristically large second-generation schizonts in both the embryonic chorioallantois and in the chicken caeca. Numerous small schizonts (10–16 µm in diameter), which contained 8–30 small merozoites, replaced the large second-generation schizonts characteristic of this species. The small schizonts were numerous 3–5 days after inoculation and were restricted to epithelial cells of the embryo allantois when sporozoites were inoculated via the allantoic cavity. These schizonts also occurred in epithelial cells of the caeca of chickens given oocysts via the crop. Cell reactions in the chicken caeca in response to infection were minimal. Numerous minute lesions were present in the chorioallantois 4–6 days after inoculation; these were associated with the small schizonts and later with gamonts and oocysts. The strain reproduced well in the embryo but failed to induce gross pathogenic effects and no mortality resulted from the infection. Only two passages of this strain in chickens were needed to restore a high degree of pathogenicity. This change was accompanied by the reappearance of the characteristically large second-generation schizonts in the tunica propria of the caecal wall.
Early inflammatory and myogenic responses to resistance exercise in the elderly

Introduction and Methods: This study compared changes in myokine and myogenic genes following resistance exercise (3 sets of 12 repetitions of maximal unilateral knee extension) in 20 elderly men (67.8 ± 1.0 years) and 15 elderly women (67.2 ± 1.5 years). Results: Monocyte chemotactic protein (MCP)‐1, macrophage inhibitory protein (MIP)‐1β, interleukin (IL)‐6 and MyoD mRNA increased significantly (P < 0.05), whereas myogenin and myostatin mRNA decreased significantly after exercise in both groups. Macrophage‐1 (Mac‐1) and MCP‐3 mRNA did not change significantly after exercise in either group. MIP‐1β, Mac‐1 and myostatin mRNA were significantly higher before and after exercise in men compared with women. In contrast, MCP‐3 and myogenin mRNA were significantly higher before and after exercise in the women compared with the men. Conclusions: In elderly individuals, gender influences the mRNA expression of certain myokines and growth factors, both at rest and after resistance exercise. These differences may influence muscle regeneration following muscle injury. Muscle Nerve 46: 407–412, 2012
Postprandial metabolism of Pacific bluefin tuna (Thunnus orientalis)

SUMMARY Specific dynamic action (SDA) is defined as the energy expended during ingestion, digestion, absorption and assimilation of a meal. This study presents the first data on the SDA response of individual tunas of any species. Juvenile Pacific bluefin tunas (Thunnus orientalis; body mass 9.7–11.0 kg; N=7) were individually fed known quantities of food consisting primarily of squid and sardine (meal energy range 1680–8749 kJ, ~4–13% of tuna body mass). Oxygen consumption rates () were measured in a swim tunnel respirometer during the postprandial period at a swimming speed of 1 body length (BL) s−1 and a water temperature of 20°C. was markedly elevated above routine levels in all fish following meal consumption [routine metabolic rate (RMR)=174±9 mg kg−1 h−1]. The peak during the SDA process ranged from 250 to 440 mg kg−1 h−1 (1.5–2.3 times RMR) and was linearly related to meal energy content. The duration of the postprandial increment in ranged from 21 h to 33 h depending upon meal energy content. Consequently, the total energy used in SDA increased linearly with meal energy and ranged from 170 kJ to 688 kJ, such that the SDA process accounted for 9.2±0.7% of ingested energy across all experiments. These values suggest rapid and efficient food conversion in T. orientalis in comparison with most other fishes. Implanted archival temperature tags recorded the increment in visceral temperature (TV) in association with SDA. returned to routine levels at the end of the digestive period 2–3 h earlier than TV. The qualitative patterns in and TV during digestion were similar, strengthening the possibility that archival measurements of TV can provide new insight into the energetics and habitat utilization of free-swimming bluefin in the natural environment. Despite efficient food conversion, SDA is likely to represent a significant component of the daily energy budget of wild bluefin tunas due to a regular and high ingestion of forage.
Assignment of CDC Weak Oxidizer Group 2 (WO-2) to the Genus Pandoraea and Characterization of Three NewPandoraea Genomospecies

ABSTRACT CDC weak oxidizer group 2 (WO-2) consists of nine phenotypically similar human clinical isolates received by the Centers for Disease Control and Prevention between 1989 and 1998. Four of the isolates were from blood, three were from sputum, and one each was from bronchial fluid and maxillary sinus. All are aerobic nonfermentative, motile gram-negative rods with one to eight polar flagella per cell. All grew at 25 and 35°C and were positive for catalase, urease (usually delayed 3 to 7 days), citrate, alkalinization of litmus milk, oxidization of glycerol (weakly), and growth on MacConkey agar and in nutrient broth without NaCl. All except one strain were oxidase positive with the Kovács method, and all except one isolate weakly oxidized d-glucose. All were negative for oxidation of d-xylose, d-mannitol, lactose, sucrose, maltose, and 20 other carbohydrates, esculin hydrolysis, indole production, arginine dihydrolase, and lysine and ornithine decarboxylase. Only two of nine isolates reduced nitrate. Broth microdilution susceptibilities were determined for all strains against 13 antimicrobial agents. Most of the strains were resistant to ampicillin, extended-spectrum cephalosporins, and aminoglycosides, including gentamicin, tobramycin, and amikacin, but they varied in their susceptibility to fluoroquinolones. High-performance liquid chromatographic and mass spectrometric analyses of the WO-2 group identified ubiquinone-8 as the major quinone component. The percent G+C of the WO-2 strains ranged from 65.2 to 70.7% (thermal denaturation method). All shared a common cellular fatty acid (CFA) profile, which was characterized by relatively large amounts (7 to 22%) of 16:1ω7c, 16:0, 17:0cyc, 18:1ω7c, and 19:0cyc11-12; small amounts (1 to 3%) of 12:0 and 14:0; and eight hydroxy acids, 2-OH-12:0 (4%), 2-OH-14:0 (trace), 3-OH-14:0 (12%), 2-OH-16:1 (1%), 2-OH-16:0 (3%), 3-OH-16:0 (4%), 2-OH-18:1 (2%), and 2-OH-19:0cyc (3%). This profile is similar to the CFA profile of Pandoraea, a recently described genus associated with respiratory infections in cystic fibrosis patients (T. Coenye et al., Int. J. Syst. Evol. Microbiol., 50:887–899, 2000). Sequencing of the 16S rRNA gene (1,300 bp) for all nine strains indicated a high level (≥98.8%) of homogeneity withPandoraea spp. type strains. DNA-DNA hybridization analysis (hydroxyapatite method; 70°C) confirmed the identity of WO-2 with the genus Pandoraea and assigned three strains toPandoraea apista and three to Pandoraea pnomenusa, and identified three additional new genomospecies containing one strain each (ATCC BAA-108, ATCC BAA-109, ATCC BAA-110). This study also shows that Pandoraea isolates may be encountered in blood cultures from patients without cystic fibrosis.
Joint Learning of the Embedding of Words and Entities for Named Entity Disambiguation

Named Entity Disambiguation (NED) refers to the task of resolving multiple named entity mentions in a document to their correct references in a knowledge base (KB) (e.g., Wikipedia). In this paper, we propose a novel embedding method specifically designed for NED. The proposed method jointly maps words and entities into the same continuous vector space. We extend the skip-gram model by using two models. The KB graph model learns the relatedness of entities using the link structure of the KB, whereas the anchor context model aims to align vectors such that similar words and entities occur close to one another in the vector space by leveraging KB anchors and their context words. By combining contexts based on the proposed embedding with standard NED features, we achieved state-of-the-art accuracy of 93.1% on the standard CoNLL dataset and 85.2% on the TAC 2010 dataset.
A novel pedestrian dead reckoning algorithm using wearable EMG sensors to measure walking strides

In personal navigation, pedestrian dead reckoning (PDR) systems based on low-cost self-contained sensors exploit the kinematics of human walking, and are well suited for indoor use and in urban canyons where GPS signals are degraded or not available. Considering the electromyography (EMG), which measures electrical potentials generated by muscle contractions from human body, would reflect the muscle activities during human locomotion, this kind of biomedical signal can be utilized to capture human walking characteristics in PDR. The work presented in this paper is the consecutive step of our pilot studies in further developing a novel and robust PDR solution using wearable EMG sensors to measure walking steps. Our PDR solution includes the EMG-based activity classification, step occurrence detection, and step length estimation, as well as the position calculation with the heading from a two-axis digital compass. To avoid step misdetection, two kinds of activities: walking normally and standing still, are classified via the hidden Markov model classifier fed by the sample entropy features extracted from the raw EMG data. Some EMG statistical parameters are also investigated to establish the optimized step length model. To validate the feasibility and effectiveness of this method, several field tests were conducted by a male tester in two experimental sessions, to demonstrate the effectiveness and practicability of the method using EMG to measure walking steps. Furthermore, the results indicate the performance of the PDR solution is comparable to that of the GPS under open-sky environments.
A New Denoising System for SONAR Images

The SONAR images are perturbed by speckle noise. The use of speckle reduction filters is necessary to optimize the image exploitation procedures. This paper presents a new denoising method in the wavelet domain, which tends to reduce the speckle, preserving the structural features and textural information of the scene. Shift-invariance associated with good directional selectivity is important for the use of a wavelet transform (WT) in many fields of image processing. Generally, complex wavelet transforms, for example, the Double Tree Complex Wavelet Transform (DT-CWT) have these useful properties. In this paper, we propose the use of the DT-CWT in association with Maximum A Posteriori (MAP) filters. Such systems carry out different quality denoising in regions with different homogeneity degree. We propose a solution for the reduction of this unwanted effect based on diversity enhancement. The corresponding denoising algorithm is simple and fast. Some simulation results prove the performance obtained.
Development and Validation of a Three-Dimensional Biomechanical Model of the Lower Extremity

One of the important applications of the computer modelling of human body is the area of joint replacement where a validated model can be used for surgery planning. It is known that the evolution of total knee and total hip replacement has been influenced to a great extent by the knowledge obtained from gait analysis studies (Andriacchi and Hurwitz, 1997). Many of the mechanical problems associated with these devices have been evaluated in terms of the mechanics of walking where the magnitude and pattern of the forces at the hip and knee joints obtained from gait analysis studies have been used as design criteria of both total hip and total knee replacements. Gait analysis provides a unique opportunity to obtain objective information that cannot be obtained through other clinical means (Andriacchi and Hurwitz, 1997). For instance, several investigators have advocated the use of gait analysis for planning surgery and therapy treatments for children with cerebral palsy (Lofterod, et al., 2007; Kay, et al., 2000; Molenaers, et al., 2006). Improvement in gait after multi-level surgery using kinematic data has been documented, while kinematics provides information on dynamic joint motion kinetics is essential for differentiating between primary deformities and secondary responses. The potential benefits of gait analysis are improved treatment decision making, so that surgery and other treatments result in improved walking capability. Also, the information generated from the gait analysis of patients with total joint replacements has been utilized as a tool for assessing recovery following these procedures, where the key to the analysis of functionality following joint replacement is the ability to identify the adaptations corresponding to the joint design features. It is very difficult to determine muscle force/power output from multiple muscles simultaneously without affecting the pattern of normal movements (Naganoa, et al., 2005). Fortunately, computer modeling can provide useful insights for human biomechanics. Most in-vivo experiments only reveal the forces in the joint and not the surrounding muscle forces or their point of application. It is also known that finding the internal forces in the body by in-vivo experiments alone is difficult and sometime impossible. Because of the inherited redundancy in the musculoskeletal system (Crowninshield and Brand, 1981b) a desired motion can be achieved by an infinite
A Comparison of Data‐Driven Groundwater Vulnerability Assessment Methods

Increasing availability of geo‐environmental data has promoted the use of statistical methods to assess groundwater vulnerability. Nitrate is a widespread anthropogenic contaminant in groundwater and its occurrence can be used to identify aquifer settings vulnerable to contamination. In this study, multivariate Weights of Evidence (WofE) and Logistic Regression (LR) methods, where the response variable is binary, were used to evaluate the role and importance of a number of explanatory variables associated with nitrate sources and occurrence in groundwater in the Milan District (central part of the Po Plain, Italy). The results of these models have been used to map the spatial variation of groundwater vulnerability to nitrate in the region, and we compare the similarities and differences of their spatial patterns and associated explanatory variables. We modify the standard WofE method used in previous groundwater vulnerability studies to a form analogous to that used in LR; this provides a framework to compare the results of both models and reduces the effect of sampling bias on the results of the standard WofE model. In addition, a nonlinear Generalized Additive Model has been used to extend the LR analysis. Both approaches improved discrimination of the standard WofE and LR models, as measured by the c‐statistic. Groundwater vulnerability probability outputs, based on rank‐order classification of the respective model results, were similar in spatial patterns and identified similar strong explanatory variables associated with nitrate source (population density as a proxy for sewage systems and septic sources) and nitrate occurrence (groundwater depth).
A cross-sectional analysis of the prevalence of dental anxiety and its relation to the oral health-related quality of life in patients with dental treatment needs at a university clinic in Switzerland.

OBJECTIVES The aim of this observational, cross-sectional study was to analyse the relationship between dental anxiety (DA) and health-related quality of life aspects associated with oral conditions of a population with dental treatment needs in Switzerland. METHODS The measurements of DA were collected by means of two questionnaires, the Dental Anxiety Scale (DAS) and a Visual Analogue Scale (VAS). Oral health-related quality of life (OHRQoL) was assessed with the Oral Health Impact Profile (OHIP). The sample included 223 patients enrolled at a university clinic which specialises in oral prosthetic rehabilitation and temporomandibular disorders. Of them, 78.9% were at or above the age of 50. RESULTS No gender or age dependencies were observed. A comparison of answers regarding OHRQoL and DA revealed a significant interdependence (p = 0.0118); highly anxious patients were 3.55 times more likely to suffer from poor quality of life compared with less anxious ones. CONCLUSION This cross-sectional study of mostly elderly patients seeking dental treatment in Switzerland found that increased DA was associated with an impaired OHRQoL. The average DA was slightly higher than the results of other industrialised countries and the average OHRQoL was reduced.
Monte Carlo simulation of the effect of shape and thickness on SEM-EDS microanalysis of asbestos fibres and bundles: the case of anthophyllite, tremolite and actinolite

Asbestos is a generic term used for six types of silicate minerals that are found in fibres or bundles of fibres, which can be easily cleaved into thinner ones. Scanning electron microscopy energy-dispersive X-ray spectrometry (SEM-EDS) quantitative microanalysis of asbestos mineral fibres still represents a complex analytical issue because of the variable fibre shape and small thickness (< 5 μm) compared with the penetration depth of the incident electron beam. Following previous work on chrysotile, crocidolite and amosite, here we present a study by means of Monte Carlo simulations of the thickness and shape effect on SEM-EDS microanalysis of anthophyllite, tremolite and actinolite asbestos. Realistic experimental conditions, such as sample geometry, SEM set-up and detector physics were taken into account. We report the results obtained on 100 μm long fibres and bundles of circular and square section and thicknesses from to 0.1 μm to 10 μm, for electron beam energies of 5, 15 and 25 keV. A strong influence of the asbestos mineral fibres and bundles shape and thickness on the detected EDS X-ray intensity was observed. In general, the X-ray intensities as a function of fibre thickness showed a considerable reduction below about 0.5 μm at 5 keV, 2 μm at 15 keV, and 5 μm at 25 keV for all the elements and minerals, with a non-linear dependence. Correction parameters, k-ratio, for the thickness effect were calculated and proposed.
A femoral model with all relevant muscles and hip capsule ligaments

In order to evaluate stabilisation systems in trochanteric femoral fractures with finite element (FE) analysis, a realistic model is required. For this purpose, a new model of a femur with all the relevant muscles and the hip capsule ligaments is set up. The pelvic and tibial bones are modelled as rigid bodies so as to take all the muscles attached to the femur into account. Fracture zones in the proximal femur are defined. Following the modelling of the geometry, the isotropic material behaviour and the load application, a numerical calculation of the femur is carried out. The static iterated FE simulation shows good agreement with in vivo data for the one-leg-stance phase during walking and Pauwels' one-leg stance regarding the displacement of the femoral head (2.9 and 5.2 mm, respectively) and the resulting hip force (253% and 294% bodyweight, respectively). In the modelled fracture zones without osteosynthesis, shear is higher than axial strain. The reduction of shear among others could be a criterion for judging the quality of a stabilisation implant.
Interdisciplinary rehabilitation after whiplash injury

Abstract Whiplash injury associated disorders (WAD) cause high costs for public health care. Neck pain is number 16 on the global prevalence lists for the 50 most common sequelae. It is of importance to obtain long-term data on disability and working capacity outcomes after rehabilitation. Long-term prospective data of the outcome course of whiplash are sparse. The aim of this study was to quantify improvements of pain, function/role performance, vitality, and working capacity 5 years after whiplash injury and to compare the state of health to normative values at 5 years after rehabilitation. In this naturalistic, observational, prospective cohort study, 115 patients were assessed 5 years (60 months) after a multidisciplinary rehabilitation program. The assessment set consisted of the Short Form 36 (SF-36), parts of the North American Spine Society's cervical spine assessment questionnaire (NASS) and the coping strategies questionnaire (CSQ). The effects were quantified by effect size (ES) and standardized response mean (SRM). Score differences over the course were tested by the Wilcoxon–Mann–Whitney U test for significance. Comparing data between entry and 60 months after rehabilitation 8 of 15 parameters improved with large ES/SRM. Outcome between 6 and 60 months showed small to moderate ES/SRM. Working capacity increased from 0 at entry to rehabilitation to 21 h/wk at 6 months and to 30 h/wk at 60 months follow-up. After large improvements in health and working capacity in the mid-term, further important improvements were observed in the long-term course. It can be hypothesized that part of those can be attributed to the interventions during inpatient rehabilitation, for example, due to better coping strategies.