Miracle-dz/UniFAR-FTUs huggingface dataset:
The selection of quantification pipelines for Illumina RNA-seq data using a subsampling approach

RNA sequencing, or (RNA-seq for short,, is a widely applied technology that for extractings gene and transcript expression from biological samples. Given numerous quantification pipelines for RNA-seq data, one fundamental challenge is to determine identify a pipeline that can produce the most accurate estimate the most accurate gene and/or transcript expression. Exploring all available pipelines requires tremendous extensive computational resources, so. Therefore, we propose to use a subsampling approach that can improve speed up the pipeline evaluation and selection the efficiency process of pipeline performance evaluation for a given RNA-seq dataset. We applied our approach to one simulated and two real RNA-seq datasets and found that expression estimates derived from subsampled data are close surrogates for those derived from original data. In addition, the ranking of quantification pipelines based on the subsampled data was highly correlated concordant with that based on the original data. Therefore, we conclude that subsampling is a valid approach to facilitating efficient quantification pipeline selection using RNA-seq data.
Intrinsic Dimension Estimation Using Packing Numbers

We propose a new algorithm to estimate the intrinsic dimension of data sets. The method is based on geometric properties of the data and requires neither parametric assumptions on the data generating model nor input parameters to set. The method is compared to a similar, widely-used algorithm from the same family of geometric techniques. Experiments show that our method is more robust in terms of the data generating distribution and more reliable in the presence of noise.
Are samples in randomized controlled trials of psychotherapy representative of community outpatients? A new methodology and initial findings.

To determine the extent to which published randomized controlled trials (RCTs) of psychotherapy can be generalized to a sample of community outpatients, the authors used a method of matching information obtained from outpatient charts to inclusion and exclusion criteria from published RCT studies. They found that 80% of the patients in their sample who had diagnoses represented in the RCT literature were judged eligible for at least 1 published RCT; however, 58% of the patients had primary diagnoses such as adjustment disorder or dysthymia, which were not represented in the existing psychotherapy outcome literature. The most common reasons that patients in their sample did not match with published RCTs for psychotherapy are listed, and the implications of these findings for research and practice are discussed.
Two-view feature generation model for semi-supervised learning

We consider a setting for discriminative semi-supervised learning where unlabeled data are used with a generative model to learn effective feature representations for discriminative training. Within this framework, we revisit the two-view feature generation model of co-training and prove that the optimum predictor can be expressed as a linear combination of a few features constructed from unlabeled data. From this analysis, we derive methods that employ two views but are very different from co-training. Experiments show that our approach is more robust than co-training and EM, under various data generation conditions.
Joint diagonalization via subspace fitting techniques

Joint diagonalization problems of Hermitian or non-Hermitian matrices occur as the final parameter estimation step in several blind source separation problems such as ACMA, JADE, PARAFAC, and SOBI. Previous approaches have been Jacobi iteration schemes and alternating projections. Here we show how the joint diagonalization problem can be formulated as a (weighted) subspace fitting problem so that it can be solved using the efficient Gauss-Newton optimization algorithm proposed for that problem. Since a good initial point is usually available, the algorithm converges very fast.
Development of a questionnaire to assess medical competencies: Reliability and validity of the Questionnaire

Introduction: While preparing a graduate survey for medical education in 2008 we realized that no instrument existed that would be suitable to evaluate whether the learning outcomes outlined in the Medical Licensure Act (ÄAppO) would be met. Therefore we developed the Freiburg Questionnaire to Assess Competencies in Medicine (Freiburger Fragebogen zur Erfassung von Kompetenzen in der Medizin, FKM)1 which has been revised and extended several times since then. Currently the FKM includes 45 items which are assigned to nine domains that correspond to the CanMEDS roles: medical expertise, communication, team-work, health and prevention, management, professionalism, learning, scholarship, and personal competencies. Methods: In order to test the reliability and validity of the questionnaire we have repeatedly surveyed medical students and residents since May 2008. In this article we report on the results of a cross-sectional study with 698 medical students from the preclinical and clinical years. In addition, we report the results of a survey of 514 residents who were up to two years into their residency. Results and conclusions: In summary, results show that the scales of the FKM are reliable (Cronbach’s α between .68 and .97). Significant differences in means between selected groups of students support the measure’s construct validity. Furthermore, there is evidence that the FKM might be used as a screening tool e.g. in graduate surveys to identify weaknesses in the medical education curriculum.
Indoor navigational aid using active RFID and QR-code for sighted and blind people

The aim of this paper is to describe a new Navigation technique to assist the blind and people with low vision to reach their destinations in an indoor environment. The proposed technique is based on our previous positioning technique using active Radio-frequency identification (RFID) technology. A Global Positioning System (GPS) does not work efficiently in indoor environments. This research produced a navigation service for sighted and blind people to assist them to reach their destination of interest via the shortest path. Tags were distributed at known locations and the mobile reader was carried by a user. The system role is to determine the shortest path to the destination which was indicated by a user. When the shortest path is calculated, the system indicates way points in the path which were represented by active tags in this scenario. Then the users are navigated to these points one by one via QR-Code till they reach their destinations. It was implemented in an indoor environment as a simulation system to navigate the user to particular offices with a successful shortest path identification rate and satisfactory navigation results were achieved.
Flow Cytometry Analysis of Intracellular VASP Phosphorylation for the Assessment of Activating and Inhibitory Signal Transduction Pathways in Human Platelets

Summary Increased platelet adhesion or aggregation are key events in the pathogenesis of cardiovascular diseases. Exact determination of the platelet activation state is essential to recognize, prevent, and treat cardiovascular complications due to platelet dysfunction. Initial phases of platelet activation and inhibition are characterized by phosphorylation of specific intracellular proteins. However, methodological problems often prevent analysis of platelet protein phosphorylation under clinical conditions. A novel flow cytometry-based method using a phosphorylation-specific antibody was developed for fast and easy quantification of the phosphorylation state of a specific intracellular platelet protein. This method was used to analyze various platelet receptors and their intracellular signaling which may be impaired in genetic or acquired disorders or altered due to therapeutic interventions. In a first clinical application, the inhibitory effects of ticlopidine and clopidogrel on the platelet P2YAC ADP receptor were monitored. Abbreviations: ADP: adenosine 5’-diphosphate; cAMP: cyclic adenosine-3’,5’-monophosphate; cGMP: cyclic guanosine-3’,5’-monophosphate; HUVECs: human umbilical vein endothelial cells; MAPK: mitogen-activated protein kinase; PG-E1: prostaglandin E1; PRP: platelet-rich plasma; SNP: sodium nitroprusside; VASP: vasodilator-stimulated phosphoprotein
Shifting, One-Inclusion Mistake Bounds and Tight Multiclass Expected Risk Bounds

Under the prediction model of learning, a prediction strategy is presented with an i.i. d. sample of n – 1 points in Χ and corresponding labels from a concept ƒ ∈ Ƒ, and aims to minimize the worst-case probability of erring on an nth point. By exploiting the structure of Ƒ, Haussler et al. achieved a VC(Ƒ)/n bound for the natural one-inclusion prediction strategy, improving on bounds implied by PAC-type results by a O(log n) factor. The key data structure in their result is the natural subgraph of the hypercube—the one-inclusion graph; the key step is a d = VC(Ƒ) bound on one-inclusion graph density. The first main result of this paper is a density bound of n (≤n-1d-1) / (≤nd) < d, which positively resolves a conjecture of Kuzmin & Warmuth relating to their unlabeled Peeling compression scheme and also leads to an improved mistake bound for the randomized (deterministic) one-inclusion strategy for all d (for d ≈ Θ(n)). The proof uses a new form of VC-invariant shifting and a group-theoretic symmetrization. Our second main result is a k-class analogue of the d/n mistake bound, replacing the VC-dimension by the Pollard pseudo-dimension and the one-inclusion strategy by its natural hypergraph generalization. This bound on expected risk improves on known PAC-based results by a factor of O (log n) and is shown to be optimal up to a O(log k) factor. The combinatorial technique of shifting takes a central role in understanding the one-inclusion (hyper)graph and is a running theme throughout.
Physical Therapy in the Emergency Department: Development of a Novel Practice Venue

Background and Purpose The American Physical Therapy Association's Vision 2020 advocates that physical therapists be integral members of health care teams responsible for diagnosing and managing movement and functional disorders. This report details the design and early implementation of a physical therapist service in the emergency department (ED) of a large, urban hospital and presents recommendations for assessing the effectiveness of physical therapists in this setting. Case Description Emergency departments serve multiple purposes in the American health care system, including care of patients with non–life-threatening illnesses. Physical therapists have expertise in screening for problems that are not amenable to physical therapy and in addressing a wide range of acute and chronic musculoskeletal pain problems. This expertise invites inclusion into the culture of ED practice. This administrative case report describes planning and early implementation of a physical therapist practice in an ED, shares preliminary outcomes, and provides suggestions for expansion and effectiveness testing of practice in this novel venue. Outcomes Referrals have increased and length of stay has decreased for patients receiving physical therapy. Preliminary surveys suggest high patient and practitioner satisfaction with physical therapy services. Outpatient physical therapy follow-up options were developed. Educating ED personnel to triage patients who show deficits in pain and functional mobility to physical therapy has challenged the usual culture of ED processes. Discussion Practice in the hospital ED enables physical therapists to fully use their knowledge, diagnostic skills, and ability to manage acute pain and musculoskeletal injury. Recommendations for future action are made to encourage more institutions across the country to incorporate physical therapy in EDs to enhance the process and outcome of nonemergent care.
Parents' narratives about their experiences of their child's reconstructive genital surgeries for ambiguous genitalia.

AIM The aim of this study was to initiate an exploration of parents' understanding and experiences of their child's reconstructive genital surgeries for ambiguous genitalia. BACKGROUND The determination of gender for a child born with ambiguous genitalia is a complex medical and social process influenced by biological, psychological, social and cultural factors. Two main approaches exist; one promotes interventions (optimal gender policy) while the other suggests delaying interventions (informed consent policy) until the child can contribute to the decision. METHODS An exploratory narrative inquiry design was chosen. Data were collected through narrative interviews with a purposive non-random sample of 10 parents of eight children (aged 0-11 years) who had ambiguous genitalia. RESULTS Parents' stories reflected strong protective instincts towards their children along with feelings of shock and disbelief. Parents' social construction of gender influenced their attitudes and beliefs about their child's ambiguous genitalia and the need for surgery. Parents' desired to be 'good parents' and do what they perceived as 'right' for their child. They considered genital surgery as a necessity primarily relying on medical advice to guide them at times of uncertainty and confusion. Parents rarely shared stories about their child's surgeries/genitalia outside of the couple relationship and these stories were often referred to as 'secrets'. CONCLUSION Having a child with ambiguous genitalia was perceived as problematic and brought about changes in roles, responsibilities, goals and social status as a parent beyond those usually associated with parenthood. RELEVANCE TO CLINICAL PRACTICE These early findings help increase awareness of parents' experiences and of the problems and emotional challenges that parents face when their child is born with genital ambiguity.
Design of optimal cascaded multirate filter banks in the presence of quantization

Classical wavelet filter banks are optimized for perfect or near-perfect reconstruction of a signal when the noise-free output of the analysis filter bank is recombined by the synthesis filter bank. Quantization gives rise to noise in the transform domain, affecting the reconstruction. This paper deals with the analysis of transform domain noise in subband systems, and the design of synthesis filters that minimize the output mean square error.
True color distributions of scene text and background

Color feature, as one of the low level features, plays important role in image processing, object recognition and other fields. For example, in the task of scene text detection and recognition, lots of methodologies employ features that utilize color contrast of text and the corresponding background for connected component extraction. However, the true distributions of text and its background, in terms of color, is still not examined because it requires an enough number of scene text database with pixel-level labelled text/non-text ground truth. To clarify the relationship between text and its background, in this paper, we aim at investigating the color non-parametric distribution of text and its background using a large database that contains 3018 scene images and 98,600 characters. The results of our experiments show that text and its background can be discriminated by means of color, therefore color feature can be used for scene text detection.
Carbohydrate analysis of the zona pellucida and cortical granules of human oocytes by means of ultrastructural cytochemistry.

BACKGROUND The zona pellucida (ZP), the mammalian oocyte coat, consists of a restricted number of highly glycosylated proteins. In vitro sperm binding studies suggest a higher binding affinity for the outer region of the ZP compared to its inner region in different species. However, the reason for this difference in binding distribution remains unresolved. Many studies suggest that the carbohydrate sequences linked to ZP glycoproteins act as ligands for sperm binding to this matrix. METHODS Lectins and antibodies that recognize different carbohydrates were employed to perform an ultrastructural analysis of human ZP and cortical granule glycosylation. RESULTS This study reveals variable glycosylation of the human ZP throughout its thickness, with pronounced differences between the most external and internal regions of this matrix. The binding studies also indicate that ZP glycoproteins express some carbohydrate sequences not previously detected in other species. Finally, cytochemical analysis of human cortical granules suggests similarities in glycosylation to ZP glycoproteins but not to cortical granules from other mammalian species. CONCLUSION A heterogeneous carbohydrate composition was observed in the thickness of the human ZP that could be responsible for the different sperm binding affinity detected between the outer and inner regions of the ZP.
Ultra-small gadolinium oxide nanocrystal sensitization of non-small-cell lung cancer cells toward X-ray irradiation by promoting cytostatic autophagy

Background Gadolinium-based nanoparticles (GdNPs) have been used as theranostic sensitizers in clinical radiotherapy studies; however, the biomechanisms underlying the radio-sensitizing effects of GdNPs have yet to be determined. In this study, ultra-small gadolinium oxide nanocrystals (GONs) were employed to investigate their radiosensitizing effects and biological mechanisms in non-small-cell lung cancer (NSCLC) cells under X-ray irradiation. Method and materials GONs were synthesized using polyol method. Hydroxyl radical production, oxidative stress, and clonogenic survival after X-ray irradiation were used to evaluate the radiosensitizing effects of GONs. DNA double-strand breakage, cell cycle phase, and apoptosis and autophagy incidences were investigated in vitro to determine the radiosensitizing biomechanism of GONs under X-ray irradiation. Results GONs induced hydroxyl radical production and oxidative stress in a dose- and concentration-dependent manner in NSCLC cells after X-ray irradiation. The sensitizer enhancement ratios of GONs ranged between 19.3% and 26.3% for the NSCLC cells under investigation with a 10% survival rate compared with that of the cells treated with irradiation alone. Addition of 3-methyladenine to the cell medium decreased the incidence rate of autophagy and increased cell survival, supporting the idea that the GONs promoted cytostatic autophagy in NSCLC cells under X-ray irradiation. Conclusion This study examined the biological mechanisms underlying the radiosensitizing effects of GONs on NSCLC cells and presented the first evidence for the radiosensitizing effects of GONs via activation of cytostatic autophagy pathway following X-ray irradiation.
Human cytomegalovirus‐specific CD8+ T‐cell expansions contain long‐lived cells that retain functional capacity in both young and elderly subjects

The immune response to human cytomegalovirus (HCMV) infection is characterized by the accumulation of HCMV‐specific CD8+ T cells, particularly in the elderly; such expansions may impair immune responses to other pathogens. We investigated mechanisms underlying HCMV‐specific expansions in 12 young and 21 old healthy subjects (although not all analyses were performed on all subjects). Phenotypically, HCMV‐pentamer+ CD8+ T cells were characterized by marked Vβ restriction, advanced differentiation (being predominantly CD27− CD28−), and variable CD45RO/RA expression. Although more common and larger in older subjects, expansions had similar phenotypic characteristics in the young. In one old subject, repeated studies demonstrated stability in size and Vβ distribution of pentamer+ populations over 6 years. We tested whether HCMV‐specific CD8+ T‐cell expansions arose from accelerated proliferation or extended lifespan by in vivo labelling with deuterated glucose and ex vivo Ki‐67 expression. Uptake of deuterated glucose was lower in pentamer+ cells than in pentamer– CD8+ CD45RO+ or CD8+ CD45RA+ cells in three old subjects, consistent with reduced proliferation and extended lifespan. Similarly Ki‐67 labelling showed no evidence for increased proliferation in HCMV‐specific CD8+ expansions in older subjects, although pentamer– CD45RA+ cells from young donors expressed very little Ki‐67. We investigated Bcl‐2 and CD95 as possible anti‐apoptotic mediators, but neither was associated with pentamer‐positivity. To investigate whether expansion represents a compensatory response to impaired functionality, we performed two tests of functionality, peptide‐stimulated proliferation and CD107 expression; both were intact in pentamer+ cells. Our data suggest that HCMV‐specific CD8+ expansions in older subjects accumulate by extended lifespan, rather than accelerated proliferation.
Scheduling Co-Design for Reliability and Energy in Cyber-Physical Systems

Energy aware scheduling and reliability are both very critical for real-time cyber-physical system design. However, it has been shown that the transient faults of a system will increase when the processor runs at reduced speed to save energy consumption. In this paper, we study total energy and reliability scheduling co-design problem for real-time cyber-physical systems. Total energy refers the sum of static and dynamic energy. Our goal is to minimize total energy while guaranteeing reliability constraints. We approach the problem from two directions based on the two different ways of guaranteeing the reliability of the tasks. The first approach aims at guaranteeing reliability at least as high as that of without speed scaling by reserving recovery job for each scaled down task. Heuristics have been used to guide the speed scaling and shutdown techniques that are used to lower total energy consumption while guaranteeing the reliability. The second way to guarantee the reliability of the tasks is to satisfy a known minimum reliability constraint for the tasks. The minimum reliable speed guarantees the reliability level of tasks, and is used as a constraint in the energy minimization problem. Both static and dynamic co-design methods are explored. Experimental results show that our methods are effective.