Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic evaluation of the efficacy–effectiveness gap of systemic treatments in metastatic nonsmall cell lung cancer

The divergence between clinical trial results and real-world outcomes is largely unknown for many cancer types. The present study aims overall to assess the efficacy–effectiveness gap (difference between outcomes in clinical trials and the real world) in systemic treatment for metastatic nonsmall cell lung cancer (NSCLC). All patients diagnosed with stage IV NSCLC between 2008 and 2014 within a network of seven Dutch large teaching hospitals (Santeon) were studied. For every patient, an efficacy–effectiveness (EE) factor was calculated by dividing individual patients' overall survival (OS) by the pooled median OS assessed from clinical trials with the respective treatment. From 2989 diagnosed patients, 1214 (41%) started with first-line treatment. For all studied regimens, real-world OS was shorter than OS reported in clinical trials. Overall, the EE factor was 0.77 (95% CI 0.70–0.85; p<0.001). Real-world patients completed their treatment plan less often and proceeded less frequently to further lines of treatment. These parameters together with Eastern Cooperative Oncology Group performance status explained 35% of the variation in EE factor. Survival of patients with metastatic NSCLC treated with chemotherapy or targeted therapy in real-world practice is nearly one-quarter shorter than for patients included in trials. Patients' performance status, earlier discontinuation and fewer subsequent lines of treatment partly explained this difference. Survival of patients with metastatic NSCLC treated with chemotherapy or targeted therapy in real-world practice is nearly one quarter shorter than for patients included in clinical trials. These real-world data provide useful information for clinicians. http://ow.ly/Khd230minFF
A closer look at heart failure in patients with concurrent diabetes mellitus using glucose lowering drugs

ABSTRACT Introduction: Type 2 diabetes (T2D) is an independent risk factor for heart failure (HF). With concomitant T2D and HF, recent data suggests an incremental risk of cardiovascular death and hospitalization for HF, as compared to patients with HF without T2D. Areas covered: Management of these two diseases has been a challenge for physicians. The treatment goals for HF patients in T2D are very important. They serve as the endpoint in using a specific treatment for management and treatment of T2D patients hence, decreasing mortality rates. In this review, we examine the effects of oral antidiabetic drugs on HF patients, discussing current evidence-based up-to-date management strategies and guidelines in the general population with HF and T2D. Expert commentary: Future in the management of T2D in HF patients looks bright. Augmenting data on potential cardiovascular side effects of antidiabetic drugs is valuable since millions of people are treated over many years. Newer novel drugs targeting specific signaling pathways are approaching the stages of clinical investigation. They have been a highly attractive concept for the future in the management of these patients. However, while advances in technology elucidated many aspects of these diseases, many mysteries still remain.
Violence With Femicide Risk: Its Effects on Women and Their Children

The objective of this study is to assess the effects that a specific type of severe violence—violence with femicide risk (VFR)—has on women’s physical and mental health, as well as the physical health of their children. I focus on Peru, a country in which 7 out of 10 women have been victims of some form of intimate partner violence. In Latin America, Peru is one of the countries with the highest rates of violence against women. Methodological gaps in the existing literature (sampling size, selection bias, and reverse causality) are covered using an important nationally representative sample (Demographic and Health Survey: N = 84,136) and the use of propensity score matching. Results show that VFR increases symptoms of depression, as well as alcohol and tobacco consumption. The children of victims of VFR had significantly more recent episodes of bloody stool, diarrhea, fever, and coughing. These effects are heterogeneous. They vary based on violence characteristics (history of sexual violence) and on victims’ socioeconomic status. According to the relevant literature, these effects can be understood to stem from somatization, stress, substance use (as a facilitator of violence), and neurological damage due to exposure to this type of violence. Results suggest VFR may have life-course altering effects given victims’ distinct coping strategies.
The influence of pitch feedback on learning of motor -timing and sequencing: A piano study with novices

Audio-motor coordination is a fundamental requirement in the learning and execution of sequential actions such as music performance. Predictive motor control mechanisms determine the sequential content and timing of upcoming tones and thereby facilitate accurate performance. To study the role of auditory-motor predictions at early stages of acquiring piano performance skills, we conducted an experiment in which non-musicians learned to play a musical sequence on the piano in synchrony with a metronome. Three experimental conditions compared errors and timing. The first consisted of normal auditory feedback using conventional piano key-to-tone mappings. The second employed fixed-pitch auditory feedback consisting of a single tone that was given with each key stroke. In the third condition, for each key stroke a tone was randomly drawn from the set of tones associated with the normal sequence. The results showed that when auditory feedback tones were randomly assigned, participants produced more sequencing errors (i.e., a higher percentage of incorrect key strokes) compared to when auditory feedback was normal or consisted of a single tone of fixed pitch. Furthermore, synchronization with the metronome was most accurate in the fixed-pitch single-tone condition. These findings suggest that predictive motor control mechanisms support sequencing and timing, and that these sensorimotor processes are dissociable even at early stages of acquiring complex motor skills such as music performance.
The Health Consequences of Social Mobility in Contemporary China

Although numerous studies have shown the importance of an individual’s socioeconomic status on his or her self-rated health status, less well-known is whether self-perceived class mobility, a measure highly correlated with an individual’s de facto social class and past mobility experiences, affects self-rated health. In this paper, we attempt to fill the gap by examining how perception of class mobility is associated with self-rated health. Using eight waves of Chinese General Social Survey data spanning the years 2005 to 2015, we conducted an analysis at the micro (individual) level and the macro (provincial) level. Analyses at both levels yielded consistent results. At the individual level, we employed ordered logistic regression and found that the perception of experiencing downward mobility was associated with significantly lower self-rated health in both rural and urban areas compared with those who consider themselves to be upwardly mobile or immobile. At the provincial level, the findings from static panel analysis further revealed that there is a positive relationship between the self-perceived class mobility and self-rated health level.
A review of the empirical studies of computer supported human-to-human communication

This paper presents a review of the empirical studies of human-to-human communication which have been carried out over the last three decades. Although this review is primarily concerned with the empirical studies of computer supported human-to-human communication, a number of studies dealing with group work in non-computer-based collaborative environments, which form the basis of many of the empirical studies of the recent years in the area of CSCW, are also discussed. The concept of person and task spaces is introduced and then subsequently used to categorise the large volume of studies reported in this review. This paper also gives a comparative analysis of the findings of these studies, and draws a number of general conclusions to guide the design and evaluation of future CSCW systems.
Risks of excess iodine intake in Ghana: current situation, challenges, and lessons for the future

In Ghana, iodine deficiency was first reported in 1994 among 33% of the population. A nationwide Universal Salt Iodization (USI) program plus other complementary interventions were subsequently implemented as a response. Our paper reviews the current risks of excess iodine status in Ghana and identifies policy and research gaps. A mixed methods review of 12 policies and institutional reports and 13 peer‐reviewed articles was complemented with consultations with 23 key informants (salt producers and distributors, food processors, regulatory agency officials, and healthcare providers) purposively sampled between May and August 2017. The findings show a strong policy environment indicated by regulations on food and salt fortification (Act 851), including the USI regulation. However, currently, only a third of Ghanaian households use adequately iodized salt. Recent evidence shows that voluntarily fortified processed foods (including condiments) supply a considerable amount of iodine to the food system. Limited biological impact data suggest possible household exposure to excessive dietary iodine (>15 parts per million). Currently, there is no systematic tracking of iodine content from fortified foods and other sources. Cross‐sectoral actions are needed to understand this situation better. Key research gap is the lack of comprehensive data on iodine content and intake from other sources in Ghana.
Understanding Collaborative Practices in the Scratch Online Community: Patterns of Participation Among Youth Designers

: Most research in massive online youth communities has focused on understanding patterns of participation and collaboration in games, social networks, and virtual worlds. Few studies have examined the nature and dynamics in amateur design communities where youth contribute content they have designed themselves. In this paper, we examine quantitative trends of participation in a youth design site focused on programming. Scratch is an online community with over 1 million registered youth designers 11-18 years of age. Drawing on a random sample of 5,000 youth programmers and their activities over three months in early 2012, we examined log files that captured the frequency of their contributions and comments on the site, making visible distinct classes of users who engaged in different sets of practices that support design on a collective scale. In the discussion we discuss implications for the design of collaborative spaces, tools, and communities.
Low Concentration of Antibiotics Modulates Gut Microbiota at Different Levels in Pre-Weaning Dairy Calves

The aim of this study was to investigate the effect of feeding milk replacer (MR) with two different antibiotics treatments on the gut microbiota of pre-weaning calves. Twelve (12) Holstein male calves at 1-day-old were randomly assigned to: milk replacer without antibiotics (CON), milk replacer plus low cocktail of antibiotics (LCA) concentration (penicillin 0.024 mg/L, streptomycin 0.025 mg/L, tetracycline 0.1 mg/L, ceftiofur 0.33 mg/L), and milk replacer plus a low concentration of single antibiotic (LSA; ceftiofur 0.33 mg/L). All the calves were harvested at 35-day-old, and the digesta from the ileum and colon was collected in addition to fecal samples. Samples were analyzed by 16S rRNA gene using Illumina MiSeq platform. Results showed that there were significant differences among treatments in the ileum, where LCA significantly reduced the relative abundance of Enterobacteriaceae (P = 0.02) especially Escherichia-coli (P = 0.02), while LSA significantly reduced the relative abundance of Comamonas (P = 0.02). In the colon and rectum, LSA treatment was significantly enriched with the class Bacilli, whereas the control group was significantly enriched with Alloprevotlla (P = 0.03). However, at the family level in the rectum LCA and LSA significantly reduced the relative abundance of Acidaminococcaceae (P = 0.01). Moreover, at the genera level in the colon, LSA significantly increased Prevotellaceae_Ga6A1_ group (P = 0.02), whereas in the rectum both of treatments reduced the relative abundance of Phascolarctobacterium (P = 0.01). In conclusion, the overall low cocktail of antibiotics concentration induced changes at different taxonomic levels; specifically the decrease in Escherichia-coli which might subsequently reduce the incidences of diarrhea in calves.
Y-Box binding protein 1 expression in breast cancer and its correlation with hormone receptors and other prognostic markers

INTRODUCTION: The present histologic and immunohistochemical prognostic markers of breast carcinoma do not effectively identify the subset of patients with poor prognosis. Y-Box binding protein 1 (YB1) is a novel biomarker which may identify and aid in targeted personalized therapy for such patients. MATERIALS AND METHODS: The study was conducted on histopathology specimens of 74 patients of breast carcinoma who had undergone modified radical mastectomy. YB1 immunohistochemistry (IHC) was performed on manual tissue microarray blocks (each having 15 cores). The YB1 expression was quantified in terms of “immunoreactive score” which was correlated with clinical parameters, hormone receptor status, and Her2neu overexpression by IHC. The Her2neu status of the equivocal cases was further evaluated by fluorescent in situ hybridization (FISH). RESULTS: YB1 was positive in 36/74 (48.6%) cases. On IHC and analysis by FISH, 25/74 (34%) cases had Her2neu overexpression. Estrogen receptor (ER) and progesterone receptor (PR) positivity was found in 42% and 36.5% cases, respectively. YB1 immunopositivity was negatively correlated with ER and PR expression, but showed a significant positive correlation with Her2neu expression. No correlation was found with other clinical parameters, tumor stage, and grade, except lymph node involvement, which showed a positive association with YB1 expression. Triple-negative breast carcinoma constituted 25.6% of the total cases, out of which 73.6% were YB1 positive. CONCLUSION: This study found that YB1 has an association with Her2neu expression. It may in future provide a therapeutic target in Her2neu overexpressing tumors.
Virtual Human: a computer graphics model for biomechanical simulations and computer-aided instruction

A comprehensive database of 3D geometric models of the human musculoskeletal anatomy has been created along with Virtual Human software that utilizes the models for both biomechanics and computer-aided instruction applications. In addition to the software, results include a lower extremity muscle model for biomechanical and rehabilitation analysis, a lumped set of muscles for rehabilitation controls systems research, an animation of knee motion including deforming muscles, and bone metabolism and muscle ion flux physiology animations for computer-aided instruction. <<ETX>>
Automatic Curation of SBML Models based on their ODE Semantics

Many models in Systems Biology are described as a system of Ordinary Differential Equations. The fact that the Systems Biology Markup Language SBML has become a standard for sharing and publishing models, has helped in making modelers formalize the structure of the reactions and use structure-related methods for reasoning about models. Unfortunately, SBML does not enforce any coherence between the structure and the kinetics of a reaction. Therefore the structural interpretation of models transcribed in SBML may vary according to different choices of representation of the original model and may be incorrect for some analyses. The first contribution of this paper is to propose a general compatibility condition between the kinetic expression and the structure of a reaction. We show that these well-formedness conditions are satisfied by standard kinetics and that they entail a property of independence from the kinetic expressions for the influence graph associated to the ODEs. We present a heuristic algorithm of low computational complexity for, given an ODE system, inferring a reaction model that preserves the ODE semantics and infers well-formed reactions whenever possible. This algorithm can be used for not only checking whether the network and ODE structures of an SBML model are consistent but also automatically curating SBML models by exporting them as ODE systems and then importing them as well-formed reaction models. We show how this strategy is capable of automatically curating SBML models on a large scale and provide some statistics figures obtained on the whole biomodels.net repository. The algorithms described in this paper are implemented in the open-source software modeling platform BIOCHAM [Fages and Soliman, 2008a, Calzone et al., 2006] available at http://contraintes.inria. fr/biocham The models used in the experiments are available from http://www.biomodels.net/
NTSHMDA: Prediction of Human Microbe-Disease Association Based on Random Walk by Integrating Network Topological Similarity

Accumulating clinic evidences have demonstrated that the microbes residing in human bodies play a significantly important role in the formation, development, and progression of various complex human diseases. Identifying latent related microbes for disease could provide insight into human disease mechanisms and promote disease prevention, diagnosis, and treatment. In this paper, we first construct a heterogeneous network by connecting the disease similarity network and the microbe similarity network through known microbe-disease association network, and then develop a novel computational model to predict human microbe-disease associations based on random walk by integrating network topological similarity (NTSHMDA). Specifically, each microbe-disease association pair is regarded as a distinct relationship level and, thus, assigned different weights based on network topological similarity. The experimental results show that NTSHMDA outperforms some state-of-the-art methods with average AUCs of 0.9070, 0.8896 <inline-formula><tex-math notation="LaTeX">$\pm$</tex-math><alternatives><mml:math><mml:mo>±</mml:mo></mml:math><inline-graphic xlink:href="luo-ieq1-2883041.gif"/></alternatives></inline-formula> 0.0038 in the frameworks of Leave-one-out cross validation and 5-fold cross validation, respectively. In case studies, 9, 18, 38 and 9, 18, 45 out of top-10, 20, 50 candidate microbes are verified by recently published literatures for asthma and inflammatory bowel disease, respectively. In conclusion, NTSHMDA has potential ability to identify novel disease-microbe associations and can also provide valuable information for drug discovery and biological researches.
A comparison between skin dose of breast cancer patients at the breast region, measured by thermoluminescent dosimeter in the presence and absence of bolus

Aim: The aim of this study was to measure entrance skin dose (ESD) on the breast of patients who had undergone radiotherapy following surgery, in the presence and absence of bolus. Materials and Methods: In this study, the ESD on the breast of 22 female patients was measured using thermoluminescent dosimeter-100 chips. For each patient, the ESD was measured 3 times (once without bolus and twice using bolus). The bolus types used in this study include super flab and wax. Results: The average ESDs on the breast of patients (from both medial and lateral tangential fields) in the presence of the super flab bolus and absence of bolus were 225.8 and 148.17 cGy, respectively, that when using the bolus, around 52% increasing in ESD was observed. The results showed a significant relationship between the ESD on the breast of patients and bolus types (P = 0.002); in addition, correlation coefficient between the two boluses (super flab and wax) was 0.615 (r = 0.615). Conclusion: When using the bolus in postmastectomy irradiation, it is noted that in dose delivery to the chest wall, surgical scar or skin of the treated region should be considered. The use of the bolus as a substance that increases of the skin dose can sometimes cause an excessive increase in skin dose that may cause severe skin reactions and underdosing of underlying tissues. Furthermore, using wax bolus in regions that do not require a lot of shaping of bolus is affordable.
ALS longitudinal studies with frequent data collection at home: study design and baseline data

Abstract Objective: To design an ALS clinical study in which patients are remotely recruited, screened, enrolled and then assessed via daily data collection at home by themselves or caregivers. Methods: This observational, natural-history study included two academic medical centers, one providing overall clinical management and the other overseeing computing and web-services design and management. Both healthy and ALS subjects were recruited on the Internet via advertisement on governmental and foundation websites as well as through Facebook and Google paid advertisements. Individuals underwent screening and enrollment remotely, including signing an electronic informed consent form. Participants were then provided self-measurement equipment and instructed on their use through a series of web-based videos. The equipment included a handgrip dynamometer, spirometer with smartphone connection, electrical impedance myography device, and an activity tracker. ALS Functional Rating Scale-Revised data were also collected. Subjects were asked to collect data daily for three months and twice-weekly for the subsequent six months. Results: One hundred and eleven ALS patients and 30 healthy individuals enrolled in the study from across 41 states (74 men, 62 women). Baseline median ALSFRS-R score was 33. Seventy two percent of the ALS patients sent equipment and 88% of the healthy subjects sent equipment were able to complete a first set of measurements. Expected baseline differences between the ALS patients and healthy participants were identified for all measures. Conclusions: It is possible to design and institute an at-home based study in ALS patients, using a number of state-of-the-art approaches, including web-based consenting and training and Internet-connected measurement devices. Trial registration: ClinicalTrials.gov identifier: NCT03016897.
Diverse serotonin actions of vilazodone reduce l‐3,4‐dihidroxyphenylalanine–induced dyskinesia in hemi‐parkinsonian rats

Background: The serotonergic system is a well‐established modulator of l‐dopa‐induced dyskinesia. To date, targeting serotonin transporters or serotonin receptor subtype 1A (5‐HT1A) reduces l‐dopa‐induced dyskinesia in animal models; however, these strategies have failed to translate clinically. Ideally, a compound acting at both known antidyskinetic sites could optimize serotonin‐mediated approaches. Vilazodone is a selective serotonin reuptake inhibitor and a partial 5‐HT1A agonist approved by the U.S. Food and Drug Administration, situating Vilazodone in a unique position to reduce l‐dopa‐induced dyskinesia without compromising l‐dopa‐mediated motor improvements.