Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Shoulder Kinematic Estimate on Joint and Muscle Mechanics Predicted by Musculoskeletal Model

<italic>Goal:</italic> Little information is available in the existing literature regarding the influence of the scapular kinematic estimate method on musculoskeletal analysis. This study aimed to assess the propagation of errors due to the method used for scapular kinematics reconstruction in the workflow of musculoskeletal modeling (joint kinematics, joint torques, muscle force, and joint reaction force) in shoulder and upper-limb movements. <italic> Methods:</italic> Two participants performed functional (arm elevation and rotation), daily life (eating and reaching pants pockets), and sports movements (a simulated throwing maneuver). Shoulder kinematics were obtained with five multibody kinematics methods: intracortical pins (<italic>Pins</italic>, reference method), International Society of Biomechanics (<italic>ISB</italic>), Jackson (<italic>Jack</italic>), Projection (<italic>Proj</italic>), and Ellipsoid (<italic>Ell</italic>) methods. For the five kinematics methods, joint torques, muscle forces, and glenohumeral joint reaction forces were computed with the Delft Shoulder and Elbow musculoskeletal model. <italic> Results:</italic> Differences up to 30° in glenohumeral joint kinematics, compared to the <italic>Pins</italic> method, resulted in differences less than 3 N.m in joint torque estimation. However, these also resulted in differences up to 50 and 831 N in the muscle force and joint reaction force estimate, respectively, in comparison to the reference method (<italic>Pins</italic>). No method yielded the worst or best results in comparison to the <italic>Pins</italic> method but the differences were task-specific. <italic>Conclusion:</italic> We concluded that shoulder biomechanical studies based on skin markers should be completed with caution when assessing joint angles, muscle forces, and glenohumeral joint reaction forces, while researchers may be more confident with the evaluation of shoulder joint torques.
Transcription Coactivators p300 and CBP Are Necessary for Photoreceptor-Specific Chromatin Organization and Gene Expression

Rod and cone photoreceptor neurons in the mammalian retina possess specialized cellular architecture and functional features for converting light to a neuronal signal. Establishing and maintaining these characteristics requires appropriate expression of a specific set of genes, which is tightly regulated by a network of photoreceptor transcription factors centered on the cone-rod homeobox protein CRX. CRX recruits transcription coactivators p300 and CBP to acetylate promoter-bound histones and activate transcription of target genes. To further elucidate the role of these two coactivators, we conditionally knocked out Ep300 and/or CrebBP in differentiating rods or cones, using opsin-driven Cre recombinase. Knockout of either factor alone exerted minimal effects, but loss of both factors severely disrupted target cell morphology and function: the unique nuclear chromatin organization seen in mouse rods was reversed, accompanied by redistribution of nuclear territories associated with repressive and active histone marks. Transcription of many genes including CRX targets was severely impaired, correlating with reduced histone H3/H4 acetylation (the products of p300/CBP) on target gene promoters. Interestingly, the presence of a single wild-type allele of either coactivator prevented many of these defects, with Ep300 more effective than Cbp. These results suggest that p300 and CBP play essential roles in maintaining photoreceptor-specific structure, function and gene expression.
Isolation and Characterization of Numerous Novel Phages Targeting Diverse Strains of the Ubiquitous and Opportunistic Pathogen Achromobacter xylosoxidans

The clinical relevance of nosocomially acquired infections caused by multi-resistant Achromobacter strains is rapidly increasing. Here, a diverse set of 61 Achromobacter xylosoxidans strains was characterized by MultiLocus Sequence Typing and Phenotype MicroArray technology. The strains were further analyzed in regard to their susceptibility to 35 antibiotics and to 34 different and newly isolated bacteriophages from the environment. A large proportion of strains were resistant against numerous antibiotics such as cephalosporines, aminoglycosides and quinolones, whereas piperacillin-tazobactam, ticarcillin, mezlocillin and imipenem were still inhibitory. We also present the first expanded study on bacteriophages of the genus Achromobacter that has been so far a blank slate with respect to phage research. The phages were isolated mainly from several waste water treatment plants in Germany. Morphological analysis of all of these phages by electron microscopy revealed a broad diversity with different members of the order Caudovirales, including the families Siphoviridae, Myoviridae, and Podoviridae. A broad spectrum of different host ranges could be determined for several phages that lysed up to 24 different and in part highly antibiotic resistant strains. Molecular characterisation by DNA restriction analysis revealed that all phages contain linear double-stranded DNA. Their restriction patterns display distinct differences underlining their broad diversity.
Clinical significance of positive Pneumocystis jirovecii polymerase chain reaction in non-human immunodeficiency virus immunocompromised patients in a real practice

Background/Aims Pneumocystis jirovecii polymerase chain reaction (PCR) can be helpful in diagnosing Pneumocystis pneumonia (PCP); however it has limitations. We evaluated the prevalence of positive P. jirovecii PCR from non-human immunodeficiency virus (HIV) immunocompromised patients and tried to determine the risk of PCP development. Methods Between May 2009 and September 2012, P. jirovecii PCR was performed in bronchoscopic specimens from 1,231 adult non-HIV immunocompromised patients suspected of respiratory infection. Only 169 patients (13.7%) who were tested positive for P. jirovecii PCR were enrolled. Retrospective chart review was performed. PCP was defined in patients with positive P. jirovecii PCR who were treated for PCP based on the clinical decision. Results From 169 P. jirovecii PCR-positive patients, 90 patients were in the PCP group (53.3%) and 79 patients were in the non-PCP group (46.7%). In the PCP group, 38% of patients expired or aggravated after therapy, whereas the majority of patients (84%) in the non-PCP group recovered without treatment for PCP. Independent risk factors for PCP by binary logistic regression analysis were underlying conditions- hematological malignancies, solid tumors or solid organ transplantation, dyspnea, age < 60 years, and albumin < 2.9 g/dL. Conclusions This study suggests that not all P. jirovecii PCR-positive patients need to be treated for PCP. Among P. jirovecii PCR-positive patients, those who are less than 60 years old, with hematological malignancies, solid tumors or solid organ transplantation, low albumin, and with symptoms of dyspnea, the possibility of PCP might be higher. Treatment should also be selected to these patients.
A view of the global conservation job market and how to succeed in it

The high demand for conservation work is creating a need for conservation‐focused training of scientists. Although many people with postsecondary degrees in biology are finding careers outside academia, many programs and mentors continue to prepare students to follow‐in‐the‐footsteps of their professors. Unfortunately, information regarding how to prepare for today's conservation‐based job market is limited in detail and scope. This problem is complicated by the differing needs of conservation organizations in both economically developed and developing regions worldwide. To help scientists identify the tools needed for conservation positions worldwide, we reviewed the current global conservation job market and identified skills required for success in careers in academia, government, nonprofit, and for‐profit organizations. We also interviewed conservation professionals across all conservation sectors. Positions in nonprofit organizations were the most abundant, whereas academic jobs were only 10% of the current job market. The most common skills required across sectors were a strong disciplinary background, followed by analytical and technical skills. Academic positions differed the most from other types of positions in that they emphasized teaching as a top skill. Nonacademic jobs emphasized the need for excellent written and oral communication, as well as project‐management experience. Furthermore, we found distinct differences across job locations. Positions in developing countries emphasized language and interpersonal skills, whereas positions in countries with advanced economies focused on publication history and technical skills. Our results were corroborated by the conservation professionals we interviewed. Based on our results, we compiled a nondefinitive list of conservation‐based training programs that are likely to provide training for the current job market. Using the results of this study, scientists may be better able to tailor their training to maximize success in the conservation job market. Similarly, institutions can apply this information to create educational programs that produce graduates primed for long‐term success.
Evaluation of Environmental Risk Due to Metro System Construction in Jinan, China

Jinan is a famous spring city in China. Construction of underground metro system may block groundwater seepage, inducing the depletion risk of springs. This paper presents an assessment of the risk due to metro line construction to groundwater in Jinan City using Analytic Hierarchy Process (AHP) and Geographic International System (GIS). Based on the characteristics of hydrogeology and engineering geology, the assessment model is established from the perspectives of surface index and underground index. The assessment results show that the high and very high risk levels of surface index exceed 98% in the north region; and high and very high risk levels of underground index exceed 56% in urban center and southern region. The assessment result also shows that about 14% of the urban area belongs to very high risk level; regions of high risk are 20% in urban area, 9% in Changqing County and 43% in Pingyin County. In the high risk region, metro lines R1 to R3, which are under construction, and metro lines L1 to L5, which are planned, have very high and high risk. Therefore, risk control measures are proposed to protect the groundwater seepage path to spring.
Test on thermal characteristics when orthogonally free machining carbon fiber reinforced plastic unidirectional laminates

In order to reveal the relationship between the cutting temperature in machining carbon fiber reinforced plastic(CFRP)and the cutting factors,orthogonally free machining tests on CFRP unidirectional laminates were conducted.The cutting temperature was measured using OMEGA-0.05 mm K type high sensitive thermocouple.Discussions were made about the effects of cutting parameters,geometric parameters of tools and material parameters on cutting temperature.The results show that cutting speed,cutting thickness,relief angle of tool and blunt radius,in the sequence of descending,have great influence on cutting temperature.The influence of cutting parameters on the temperature is not affected by the fiber orientation angle.Unlike metal materials,the cutting temperature is greatly influenced by CFRP fiber orientation angle.The cutting temperature cut along fiber orientation is significantly higher than that opposite fiber orientation.The maximum cutting temperature is present to the fiber orientation angle of 90°,and the cutting temperature at the fiber orientation angle of 90°is 2times of that at the fiber orientation angle of 0°. The spring back of CFRP has great influence on the contact condition between the tool flank and the machined surface,which will affect the cutting temperature eventually.This has exacerbated the anisotropy of the cutting temperature.Moreover,the heat in the third deformation zone has prominent effect on cutting temperature.CFRP has a narrow cutting temperature range,maximum cutting temperature is about 300 ℃,which will make cutting quality more sensitive to temperature changes.
Validation of Inspection Reviews over Variable Features Set Threshold

Background: Mining software requirement reviews involve natural language processing (NLP) to efficiently validate a true-fault as useful and false-positive as non-useful. Aim: The aim of this paper is to evaluate our proposed mining approach to automate the validation of requirement reviews generated during an inspection of NL requirements document. Method: Our approach utilized two training models; one from requirement reviews and other from online movies. We conducted an empirical study to test our approach using part of speech (POS) against these two trained models and observed trends w.r. t. F-measure and G-mean along with percentage of features used to train two models. Results: The results showed that using training reviews from two different domains report similar trend across evaluation metrics. Our results show that the most stable and promising validation results for F-measure and G-mean are obtained when a model over inspection and movies reviews are trained using feature set threshold value 65% and 45% respectively.
Engaging patients and families in communication across transitions of care: an integrative review protocol.

AIM To describe an integrative review protocol to analyse and synthesize peer-reviewed research evidence in relation to engagement of patients and their families in communication during transitions of care to, in and from acute care settings. BACKGROUND Communication at transitions of care in acute care settings can be complex and challenging, with important information about patients not always clearly transferred between responsible healthcare providers. Involving patients and their families in communication during transitions of care may improve the transfer of clinical information and patient outcomes and prevent adverse events during hospitalization and following discharge. Recently, optimizing patient and family participation during care transitions has been acknowledged as central to the implementation of patient-centred care. DESIGN Integrative review with potential for meta-analysis and application of framework synthesis. REVIEW METHOD The review will evaluate and synthesize qualitative and quantitative research evidence identified through a systematic search. Primary studies will be selected according to inclusion criteria. Data collection, quality appraisal and analysis of the evidence will be conducted by at least two authors. Nine electronic databases (including CINAHL and Medline) will be searched. The search will be restricted to 10 years up to December 2013. Data analysis will include content and thematic analysis. DISCUSSION The review will seek to identify all types of patient engagement activities employed during transitions of care communication. The review will identify enablers for and barriers to engagement for patients, families and health professionals. Key strategies and tools for improving patient engagement, clinical communication and promoting patient-centred care will be recommended based on findings.
Persistent DNA strand breaks induce a CAF-like phenotype in normal fibroblasts

Cancer-associated fibroblasts (CAFs) are an emerging target for cancer therapy as they promote tumour growth and metastatic potential. However, CAF targeting is complicated by the lack of knowledge-based strategies aiming to selectively eliminate these cells. There is a growing body of evidence suggesting that a pro-inflammatory microenvironment (e.g. ROS and cytokines) promotes CAF formation during tumorigenesis, although the exact mechanisms involved remain unclear. In this study, we reveal that a prolonged pro-inflammatory stimulation causes a de facto deficiency in base excision repair, generating unrepaired DNA strand breaks and thereby triggering an ATF4-dependent reprogramming of normal fibroblasts into CAF-like cells. Based on the phenotype of in vitro-generated CAFs, we demonstrate that midostaurin, a clinically relevant compound, selectively eliminates CAF-like cells deficient in base excision repair and prevents their stimulatory role in cancer cell growth and migration.
An Electrowetting Model for Rough Surfaces Under Low Voltage

Electrowetting is one of the most effective methods to enhance wettability. A significant change of contact angle for the liquid droplet can result from the surface microstructures and the external electric field, without altering the chemical composition of the system. During the electrowetting process on a rough surface, the droplet exhibits a sharp transition from the Cassie–Baxter to the Wenzel regime at a low critical voltage. In this paper, a theoretical model for electrowetting is put forth to describe the dynamic electrical control of the wetting behavior at the low voltage, considering the surface topography. The theoretical results are found to be in good agreement with the existing experimental results.
Exploring the Influence of Carbon Nanoparticles on the Formation of β-Sheet-Rich Oligomers of IAPP22–28 Peptide by Molecular Dynamics Simulation

Recent advances in nanotechnologies have led to wide use of nanomaterials in biomedical field. However, nanoparticles are found to interfere with protein misfolding and aggregation associated with many human diseases. It is still a controversial issue whether nanoparticles inhibit or promote protein aggregation. In this study, we used molecular dynamics simulations to explore the effects of three kinds of carbon nanomaterials including graphene, carbon nanotube and C60 on the aggregation behavior of islet amyloid polypeptide fragment 22–28 (IAPP22–28). The diverse behaviors of IAPP22–28 peptides on the surfaces of carbon nanomaterials were studied. The results suggest these nanomaterials can prevent β-sheet formation in differing degrees and further affect the aggregation of IAPP22–28. The π–π stacking and hydrophobic interactions are different in the interactions between peptides and different nanoparticles. The subtle differences in the interaction are due to the difference in surface curvature and area. The results demonstrate the adsorption interaction has competitive advantages over the interactions between peptides. Therefore, the fibrillation of IAPP22–28 may be inhibited at its early stage by graphene or SWCNT. Our study can not only enhance the understanding about potential effects of nanomaterials to amyloid formation, but also provide valuable information to develop potential β-sheet formation inhibitors against type II diabetes.
The long non-coding RNA PARROT is an upstream regulator of c-Myc and affects proliferation and translation

Long non-coding RNAs are important regulators of gene expression and signaling pathways. The expression of long ncRNAs is dysregulated in cancer and other diseases. The identification and characterization of long ncRNAs is often challenging due to their low expression level and localization to chromatin. Here, we identify a functional long ncRNA, PARROT (Proliferation Associated RNA and Regulator Of Translation) transcribed by RNA polymerase II and expressed at a relatively high level in a number of cell lines. The PARROT long ncRNA is associated with proliferation in both transformed and normal cell lines. We characterize the long ncRNA PARROT as an upstream regulator of c-Myc affecting cellular proliferation and translation using RNA sequencing and mass spectrometry following depletion of the long ncRNA. PARROT is repressed during senescence of human mammary epithelial cells and overexpressed in some cancers, suggesting an important association with proliferation through regulation of c-Myc. With this study, we add to the knowledge of cytoplasmic functional long ncRNAs and extent the long ncRNA-Myc regulatory network in transformed and normal cells.
Is the sunny side up and the dark side down? Effects of stimulus type and valence on a spatial detection task

ABSTRACT In verbal communication, affective information is commonly conveyed to others through spatial terms (e.g. in “I am feeling down”, negative affect is associated with a lower spatial location). This study used a target location discrimination task with neutral, positive and negative stimuli (words, facial expressions, and vocalizations) to test the automaticity of the emotion-space association, both in the vertical and horizontal spatial axes. The effects of stimulus type on emotion-space representations were also probed. A congruency effect (reflected in reaction times) was observed in the vertical axis: detection of upper targets preceded by positive stimuli was faster. This effect occurred for all stimulus types, indicating that the emotion-space association is not dependent on sensory modality and on the verbal content of affective stimuli.
High “Normal” Blood Glucose Is Associated with Decreased Brain Volume and Cognitive Performance in the 60s: The PATH through Life Study

Context Type 2 diabetes is associated with cerebral atrophy, cognitive impairment and dementia. We recently showed higher glucose levels in the normal range not to be free of adverse effects and to be associated with greater hippocampal and amygdalar atrophy in older community-dwelling individuals free of diabetes. Objective This study aimed to determine whether blood glucose levels in the normal range (<6.1 mmol/L) were associated with cerebral volumes in structures other than the hippocampus and amygdale, and whether these glucose-related regional volumes were associated with cognitive performance. Design, Setting and Participants 210 cognitively healthy individuals (68–73 years) without diabetes, glucose intolerance or metabolic syndrome were assessed in the large, community-based Personality and Total Health Through Life (PATH) study. Main Outcome Measure Baseline blood glucose levels in the normal range (3.2–6.1 mmol/l) were used to determine regional brain volumes and associated cognitive function at wave 3. Results Higher blood glucose levels in the normal range were associated with lower grey/white matter regional volumes in the frontal cortices (middle frontal gyrus, inferior frontal gyrus precentral gyrus). Moreover, identified cerebral regions were associated with poorer cognitive performance and the structure-function associations were gender specific to men. Conclusion These findings stress the need to re-evaluate what is considered as healthy blood glucose levels, and consider the role of higher normal blood glucose as a risk factor for cerebral health, cognitive function and dementia. A better lifetime management of blood glucose levels may contribute to improved cerebral and cognitive health in later life and possibly protect against dementia.
Extracting Lexical-Semantic Knowledge from the Portuguese Wiktionary

Public domain collaborative resources like Wiktionary and Wikipedia have recently become attractive sources for information extraction. To use these resources in natural languague processing (NLP) tasks, efficient programmatic access to their contents is required. In this work, we have extracted semantic relations automatically from the Portuguese Wiktionary and compared our results with the relations in PAPEL, a public domain lexical network extracted from a proprietary dictionary. We have found about 44,000 relations that were not in PAPEL, which suggests that Wiktionary is a valuable alternative source for enriching existing lexical knowledge bases.