LLukas22/scidocs huggingface dataset:
An overview of topic modeling and its current applications in bioinformatics

BACKGROUND
With the rapid accumulation of biological datasets, machine learning methods designed to automate data analysis are urgently needed. In recent years, so-called topic models that originated from the field of natural language processing have been receiving much attention in bioinformatics because of their interpretability. Our aim was to review the application and development of topic models for bioinformatics.


DESCRIPTION
This paper starts with the description of a topic model, with a focus on the understanding of topic modeling. A general outline is provided on how to build an application in a topic model and how to develop a topic model. Meanwhile, the literature on application of topic models to biological data was searched and analyzed in depth. According to the types of models and the analogy between the concept of document-topic-word and a biological object (as well as the tasks of a topic model), we categorized the related studies and provided an outlook on the use of topic models for the development of bioinformatics applications.


CONCLUSION
Topic modeling is a useful method (in contrast to the traditional means of data reduction in bioinformatics) and enhances researchers' ability to interpret biological information. Nevertheless, due to the lack of topic models optimized for specific biological data, the studies on topic modeling in biological data still have a long and challenging road ahead. We believe that topic models are a promising method for various applications in bioinformatics research.
The population prevalence of symptomatic radiographic foot osteoarthritis in community-dwelling older adults: cross-sectional findings from the Clinical Assessment Study of the Foot

OBJECTIVES
To estimate the population prevalence of symptomatic radiographic osteoarthritis (OA) affecting the 1st metatarsophalangeal joint (MTPJ), 1st and 2nd cuneometatarsal joints (CMJs), navicular first cuneiform joint (NCJ) and talonavicular joint (TNJ) in community-dwelling older adults.


METHODS
9334 adults aged ≥50 years registered with four general practices were mailed a health survey. Responders reporting foot pain within the last 12 months were invited to undergo weight-bearing dorso-plantar and lateral radiographs of both feet. OA at the 1st MTPJ, 1st and 2nd CMJs, NCJ and TNJ was graded using a validated atlas. Population prevalence estimates for symptomatic radiographic foot OA overall and for each joint were calculated using multiple imputation and weighted logistic regression modelling to account for missing data and non-response.


RESULTS
5109 health surveys were received (adjusted response 56%). Radiographs were obtained on 557 participants. Overall population prevalence of symptomatic radiographic OA was 16.7% (95% CI 15.3% to 18.0%), 1st MTPJ 7.8% (6.7% to 8.9%), 1st CMJ 3.9% (2.9% to 4.9%), 2nd CMJ 6.8% (5.7% to 7.8%), NCJ 5.2% (4.0% to 6.4%) and TNJ 5.8% (4.8% to 6.9%). With the exception of the 1st CMJ, prevalence was greater in females than males, increased with age and was higher in lower socioeconomic classes. Three-quarters of those with symptomatic radiographic OA reported disabling foot symptoms.


CONCLUSIONS
While cautious interpretation due to non-response is warranted, our study suggests that symptomatic radiographic foot OA affects one in six older adults and the majority report associated disability. Clinicians should consider OA as a possible cause of chronic foot pain in older people.
[Transrectal biopsy scheme can predict incorrect histological grading in prostate cancer].

OBJECTIVE
To identify factors that might explain why a prostate with a Gleason score (GS) <7 in the biopsy specimen can turn out to have a GS ≥7 in the surgical specimen.


MATERIAL AND METHODS
We compared the GS of biopsy specimens with the GS of surgical specimens in 185 patients who underwent surgery for prostate cancer. We calculated the sensitivity, specificity, and predictive values for the GS of the biopsy specimens. We used Cohen's kappa to determine the degree of concordance between a GS of <7 and ≥7 for the biopsy specimen and the surgical specimen. Age, a family history of prostate cancer, total prostate-specific antigen (tPSA), digital rectal examination, prostate structure and volume, and the number of biopsy cores (biopsy scheme) were analyzed using multivariable logistic regression.


RESULTS
Histological study of biopsy specimens yielded high sensitivity (98%) but low specificity (49%) for GS ≤6 and low sensitivity (35, 26%) and high specificity (93, 99%) for GS=7 and GS ≥7, respectively. Cohen's kappa for the GS from the biopsy and surgical specimens was 0.43 (95% CI=30-56%). The biopsy scheme was the only predictor of discordance in the GS between the two techniques. Among the other variables included in the model, only tPSA showed a slightly significant association. Taking a scheme with less than 7 cores as a reference, we found no difference with 8 to 9 cores but we did find a difference with 10 to 11 cores and with 12 or more cores, with a prevalence ratio of 0.138 (95% CI=0.030-0.513) and 0.277 (95% CI=0.091-0.806), respectively.


CONCLUSION
The GS of the biopsy depends on the scheme. This factor must be taken into account when choosing a treatment option in patients with low tumor grade in biopsy specimens.
Outcome of bonded vs all-ceramic and metal- ceramic fixed prostheses for single tooth replacement.

AIM
The conventional treatment of a single missing tooth is most frequently based on the provision of a fixed dental prosthesis (FDPs). A variety of designs and restorative materials are available which have an impact on the treatment outcome. Consequently, it was the aim of this review to compare resin-bonded, all-ceramic and metal-ceramic FDPs based on existing evidence.


MATERIALS AND METHODS
An electronic literature search using "metal-ceramic" AND "fixed dental prosthesis" AND "clinical, all-ceramic" AND "fixed dental prosthesis" AND "clinical, resin-bonded" AND "fixed dental prosthesis" AND "clinical, fiber reinforced composite" AND "clinical, monolithic" AND "zirconia" AND "clinical" was conducted and supplemented by the manual searching of bibliographies from articles already included.


RESULTS
A total of 258 relevant articles were identified. Metal-ceramic FDPs still show the highest survival rates of all tooth-supported restorations. Depending on the ceramic system used, all-ceramic restorations may reach comparable survival rates while the technical complications, i.e. chipping fractures of veneering materials in particular, are more frequent. Resin-bonded FDPs can be seen as long-term provisional restorations with the survival rate being higher in anterior locations and when a cantilever design is applied. Inlay-retained FDPs and the use of fiber-reinforced composites overall results in a compromised long-term prognosis. Recently advocated monolithic zirconia restorations bear the risk of low temperature degradation.


CONCLUSIONS
Several variables affect treatment planning for a given patient situation, with survival and success rates of different restorative options representing only one factor. The broad variety of designs and materials available for conventional tooth-supported restorations should still be considered as a viable treatment option for single tooth replacement.
A preliminary validation of the Brief COPE instrument for assessing coping strategies among people living with HIV in China

BACKGROUND
The Brief COPE instrument has been utilized to conduct research on various populations, including people living with HIV (PLWH). However, the questionnaire constructs when applied to PLWH have not been subjected to thorough factor validation.


METHODS
A total of 258 PLWH were recruited from two provinces of China. They answered questions involving the scales of three instruments: the Brief COPE, the Perceived Social Support Scale, and the Perceived Discrimination Scale for PLWH. Confirmatory factor analysis (CFA) and exploratory factor analysis (EFA) were conducted.


RESULTS
The CFA found a poor goodness of fit to the data. The subsequent EFA identified six preliminary factors, forming subscales with Cronbach's alphas, which ranged from 0.61 to 0.80. Significant correlation coefficients between the subscales and measures of perceived social support and perceived discrimination were reported, giving preliminary support to the validity of the new empirical factor structure.


CONCLUSION
This study showed that the original factor structure of the Brief COPE instrument, when applied to PLWH in China, did not fit the data. Thus, the Brief COPE should be applied to various populations and cultures with caution. The new factor structure established by the EFA is only preliminary and requires further validation.
Induction and maintenance of self tolerance: the role of CD4+CD25+ regulatory T cells

The immune system responds vigorously to invading pathogens (non-self, foreign), while remaining unresponsive (tolerant) to the body’s own components and circulating constituents (self). This indifference to self components is a result of finely orchestrated events of thymic negative selection (central tolerance) of developing T cells that are autoaggressive combined with those operative in the periphery (peripheral tolerance) to control the activity of potentially autoreactive T cells that escaped thymic tolerance. Recently, autoimmune regulator expressed in the thymus has been identified as a critical mediator of central tolerance towards tissue-specific antigens. In the periphery, a variety of regulatory T cells are involved in effecting tolerance. There is immense interest and excitement about the newly identified subset of CD4+CD25+ T cells. This is a unique subset of CD4+ T cells that bear CD25 (IL-2Rα chain) on the cell surface in the naïve state and express FoxP3 as a unique marker. These cells suppress the activity of autoreactive effector T cells primarily via cell-cell contact. The deficiency and/or altered function of CD4+CD25+ T cells is associated with autoimmunity. Mice deficient in FoxP3 (scurfy mice) bear an autoimmune phenotype, and human males with mutations in the corresponding gene express the phenotype of wide-spread autoimmunity, the immune dysregulation, polyendocrinopathy and enteropathy, and X-linked syndrome. In vitro expansion of antigen-specific CD4+CD25+ T cells and their adoptive transfer into patients suffering from autoimmunity is emerging as a promising new therapeutic approach for these debilitating disorders.
Deep inelastic eγ scattering at high Q2

Abstract The electromagnetic and weak structure functions of the photon can be studied in the deep inelastic electron-photon processes eγ → e + X and eγ → ν + X . While at low energies only virtual photon exchange is operative in the neutral-current process, additional Z -exchange becomes relevant for high Q 2 of order M Z 2 at e + e − linear colliders. Likewise the charged-current process can be observed at these high energy colliders. By measuring the electroweak neutral- and charged-current structure functions, the up- and down-type quark content of the photon can be determined separately.
Superiority of clopidogrel versus aspirin in patients with prior cardiac surgery.

BACKGROUND
After coronary artery bypass surgery, patients have a high cumulative rate of graft closure and recurrent ischemic events. We sought to determine whether antiplatelet therapy with clopidogrel would be more effective than aspirin, the accepted standard, in these patients.


METHODS AND RESULTS
The event rates for all-cause mortality, vascular death, myocardial infarction, stroke, and rehospitalization were determined for the 1480 patients with a history of cardiac surgery randomized to either clopidogrel or aspirin in a trial of 19 185 patients. The event rate per year of vascular death, myocardial infarction, stroke, or rehospitalization was 22.3% in the 705 patients randomized to aspirin and 15.9% in the 775 patients randomized to clopidogrel (P:=0.001). A risk reduction was also seen in each of the individual end points examined, including a 42.8% relative risk reduction in vascular death in patients on clopidogrel versus aspirin (P:=0.030). In a multivariate model incorporating baseline clinical characteristics, clopidogrel therapy was independently associated with a decrease in vascular death, myocardial infarction, stroke, or rehospitalization in patients with a history of cardiac surgery, with a 31.2% relative risk reduction (95% CI, 15.8 to 43.8; P:=0.0003). Although clopidogrel therapy was efficacious in the entire Clopidogrel Versus Aspirin in Patients at Risk of Ischemic Events (CAPRIE) population, multivariate analysis demonstrated that patients with previous cardiac surgery derived particular benefit (P:=0.015).


CONCLUSION
Compared with aspirin, clopidogrel therapy results in a striking reduction in the elevated risk for recurrent ischemic events seen in patients with a history of prior cardiac surgery, along with a decreased risk of bleeding.
NOMA in 5G Systems: Exciting Possibilities for Enhancing Spectral Efficiency

This article provides an overview of power-domain non-orthogonal multiple access for 5G systems. The basic concepts and benefits are briefly presented, along with current solutions and standardization activities. In addition, limitations and research challenges are discussed.
NFV: state of the art, challenges, and implementation in next generation mobile networks (vEPC)

As mobile network users look forward to the connectivity speeds of 5G networks, service providers are facing challenges in complying with connectivity demands without substantial financial investments. Network function virtualization (NFV) is introduced as a new methodology that offers a way out of this bottleneck. NFV is poised to change the core structure of telecommunications infrastructure to be more cost-efficient. In this article, we introduce an NFV framework, and discuss the challenges and requirements of its use in mobile networks. In particular, an NFV framework in the virtual environment is proposed. Moreover, in order to reduce signaling traffic and achieve better performance, this article proposes a criterion to bundle multiple functions of a virtualized evolved packet core in a single physical device or a group of adjacent devices. The analysis shows that the proposed grouping can reduce the network control traffic by 70 percent.
Real time tracking using an active pan-tilt-zoom network camera

We present here a real time active vision system on a PTZ network camera to track an object of interest. We address two critical issues in this paper. One is the control of the camera through network communication to follow a selected object. The other is to track an arbitrary type of object in real time under conditions of pose, viewpoint and illumination changes. We analyze the difficulties in the control through the network and propose a practical solution for tracking using a PTZ network camera. Moreover, we propose a robust real time tracking approach, which enhances the effectiveness by using complementary features under a two-stage particle filtering framework and a multi-scale mechanism. To improve time performance, the tracking algorithm is implemented as a multi-threaded process in OpenMP. Comparative experiments with state-of-the-art methods demonstrate the efficiency and robustness of our system in various applications such as pedestrian tracking, face tracking, and vehicle tracking.
Neoliberal restructuring: The Origin and Formation of Economic Groups in Chile

In modern day Chile the economic entrepreneurial landscape is made up of large multinational conglomerates, local economic groups, and so-called emerging economic groups (that burgeoned with the tr...
Pilot randomized controlled trial: elastic-resistance-training and lifestyle-activity intervention for sedentary older adults.

The aim of this study was to determine the efficacy and feasibility of a resistance-training (RT) and lifestyle-activity program for sedentary older adults. Eligible participants (N = 44) were randomized to an 8-wk intervention or a control group. The primary outcome was lower body muscle strength, and participants completed a range of secondary outcomes. There was a significant group-by-time interaction for lower body muscle strength (difference = 3.9 repetitions [reps], 95% CI = 2.0-5.8 reps; p < .001; d = 1.0). Changes in secondary outcomes were generally small and not statistically significant. Attendance and program satisfaction were both high. A combined elastic-tubing RT and lifestyle-activity program delivered in the community setting is an efficacious and feasible approach to improve health in sedentary older adults.
Race/ethnic differences in exposure to traumatic events, development of post-traumatic stress disorder, and treatment-seeking for post-traumatic stress disorder in the United States.

BACKGROUND
To identify sources of race/ethnic differences related to post-traumatic stress disorder (PTSD), we compared trauma exposure, risk for PTSD among those exposed to trauma, and treatment-seeking among Whites, Blacks, Hispanics and Asians in the US general population.


METHOD
Data from structured diagnostic interviews with 34 653 adult respondents to the 2004-2005 wave of the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) were analysed.


RESULTS
The lifetime prevalence of PTSD was highest among Blacks (8.7%), intermediate among Hispanics and Whites (7.0% and 7.4%) and lowest among Asians (4.0%). Differences in risk for trauma varied by type of event. Whites were more likely than the other groups to have any trauma, to learn of a trauma to someone close, and to learn of an unexpected death, but Blacks and Hispanics had higher risk of child maltreatment, chiefly witnessing domestic violence, and Asians, Black men, and Hispanic women had higher risk of war-related events than Whites. Among those exposed to trauma, PTSD risk was slightly higher among Blacks [adjusted odds ratio (aOR) 1.22] and lower among Asians (aOR 0.67) compared with Whites, after adjustment for characteristics of trauma exposure. All minority groups were less likely to seek treatment for PTSD than Whites (aOR range: 0.39-0.61), and fewer than half of minorities with PTSD sought treatment (range: 32.7-42.0%).


CONCLUSIONS
When PTSD affects US race/ethnic minorities, it is usually untreated. Large disparities in treatment indicate a need for investment in accessible and culturally sensitive treatment options.
Facial rejuvenation surgery: a retrospective study of 8788 cases.

BACKGROUND
Surgical rejuvenation of the aging face is common in aesthetic surgery, and many surgical techniques have been described for accomplishing it. The keys to consistent results are the surgeon's judgment and ability to individualize a treatment plan according to the patient's needs. To obtain natural-appearing results, the surgeon must consider the morphological characteristics of the aging face.


OBJECTIVES
The authors describe their approach for "round" facelift technique and strategies for avoiding complications.


METHODS
This retrospective study included 8788 consecutive patients who underwent facelift procedures in a single clinic between 1958 and 2010. All cases involved the round-lifting technique.


RESULTS
Patients in this series ranged in age from 28 to 84 years. The percentage of male patients increased in later years (6.3% in 1970-1974 vs 18.6% in 1986-2010), and there was a trend toward increasing age after 1979 (17.7% of patients aged 60 years or older vs 8.3% before 1980). Submental liposuction was the most common facelift procedure performed (92.2% of patients, 1990-2010). Up to 97% of the cases treated after 1999 underwent repositioning of the malar fat pad. The overall complication rate was 4.5%, with the most frequent complications being hematoma (3%) and cutaneous slough or necrosis (1%).


CONCLUSIONS
Repositioning the vector connecting the tragus with the Darwin tubercle provides more natural correction of aging tissues than do other techniques. The authors' intent was to keep the structures in their natural location, as they had been prior to aging. Superficial musculo-aponeurotic system (SMAS) plication, malar fat pad repositioning, and correct traction of facial tissues showed satisfactory results. This technique is less aggressive than undermining of the SMAS and deep-plane techniques.


LEVEL OF EVIDENCE
4.
Patient knowledge of atrial fibrillation: 3-month follow-up after an emergency room visit.

AIM
This paper is a report of a study to assess patient knowledge about atrial fibrillation, its determinants and evolution during 3 months after a visit to the emergency room.


BACKGROUND
Atrial fibrillation is one of the most common single diagnoses in the emergency room, and care often results in treatment modifications after which most patients are discharged home.


METHOD
A knowledge test was developed to measure patients' knowledge of atrial fibrillation. Patient data from 200 patients were assessed by examining quartiles and medians. The statistical significance of changes was tested with the Sign test. A logistic regression model was built to identify variables possibly related to patient knowledge. The data were collected in 2003 in three emergency rooms in Finland.


RESULTS
Patients had only moderate knowledge about atrial fibrillation in the emergency room, and their knowledge showed only limited improvement 3 months after the visit. They had best knowledge of the symptoms of atrial fibrillation and its effects on everyday life. There were gaps in their knowledge about this disease and how it is treated, including anticoagulation, detection of symptoms and when to seek treatment, both during the emergency room visit and 3 months thereafter. Male gender, previous atrial fibrillation diagnosis and sense of good coping with the disease were statistically significantly associated with better knowledge.


CONCLUSION
Informational support should be available for patients with atrial fibrillation during and after the emergency room visit. The knowledge test introduced in this paper could be developed to evaluate the educational needs of individual patients.
Tocotrienol rich fraction supplementation improved lipid profile and oxidative status in healthy older adults: A randomized controlled study

BACKGROUND
Vitamin E supplements containing tocotrienols are now being recommended for optimum health but its effects are scarcely known. The objective was to determine the effects of Tocotrienol Rich Fraction (TRF) supplementation on lipid profile and oxidative status in healthy older individuals at a dose of 160 mg/day for 6 months.


METHODS
Sixty-two subjects were recruited from two age groups: 35-49 years (n = 31) and above 50 years (n = 31), and randomly assigned to receive either TRF or placebo capsules for six months. Blood samples were obtained at 0, 3rd and 6th months.


RESULTS
HDL-cholesterol in the TRF-supplemented group was elevated after 6 months (p < 0.01). Protein carbonyl contents were markedly decreased (p < 0.001), whereas AGE levels were lowered in the > 50 year-old group (p < 0.05). Plasma levels of total vitamin E particularly tocopherols were significantly increased in the TRF-supplemented group after 3 months (p < 0.01). Plasma total tocotrienols were only increased in the > 50 year-old group after receiving 6 months of TRF supplementation. Changes in enzyme activities were only observed in the > 50 year-old group. SOD activity was decreased after 3 (p < 0.05) and 6 (p < 0.05) months of TRF supplementation whereas CAT activity was decreased after 3 (p < 0.01) and 6 (p < 0.05) months in the placebo group. GPx activity was increased at 6 months for both treatment and placebo groups (p < 0.05).


CONCLUSION
The observed improvement of plasma cholesterol, AGE and antioxidant vitamin levels as well as the reduced protein damage may indicate a restoration of redox balance after TRF supplementation, particularly in individuals over 50 years of age.