Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulatory Control or Oxidative Damage? Proteomic Approaches to Interrogate the Role of Cysteine Oxidation Status in Biological Processes*

Oxidation is a double-edged sword for cellular processes and its role in normal physiology, cancer and aging remains only partially understood. Although oxidative stress may disrupt biological function, oxidation-reduction (redox) reactions in a cell are often tightly regulated and play essential physiological roles. Cysteines lie at the interface between these extremes since the chemical properties that make specific thiols exquisitely redox-sensitive also predispose them to oxidative damage by reactive oxygen or nitrogen species during stress. Thus, these modifications can be either under reversible redox regulatory control or, alternatively, a result of reversible or irreversible oxidative damage. In either case, it has become increasingly important to assess the redox status of protein thiols since these modifications often impact such processes as catalytic activity, conformational alterations, or metal binding. To better understand the redox changes that accompany protein cysteine residues in complex biological systems, new experimental approaches have been developed to identify and characterize specific thiol modifications and/or changes in their overall redox status. In this review, we describe the recent technologies in redox proteomics that have pushed the boundaries for detecting and quantifying redox cysteine modifications in a cellular context. While there is no one-size-fits-all analytical solution, we highlight the rationale, strengths, and limitations of each technology in order to effectively apply them to specific biological questions. Several technological limitations still remain unsolved, however these approaches and future developments play an important role toward understanding the interplay between oxidative stress and redox signaling in health and disease.
Hodgkin disease: prognostic factors and treatment strategies

Depending on stage and risk factor profile, more than 80% of patients with Hodgkin disease (HD) will be cured with modern treatment strategies. In early-stage, favorable HD, extended field irradiation has been the standard treatment resulting in cure rates of greater than 90%. However, due to the recognition of fatal long-term effects, especially the high rates of second solid tumors, extended field irradiation therapy is now being abandoned by most study groups. Instead, mild chemotherapy for control of occult disease is combined with involved field irradiation. In early-stage, unfavorable (intermediate) HD, for which combined modality treatment is already the treatment of choice, extended field irradiation is replaced by involved field irradiation for the same reasons. A different situation is found in advanced HD. In this case, standard therapy consists of eight cycles of polychemotherapy. Until recently, modifications of the standard chemotherapy regimens had not changed the poor outcome of advanced-stage patients. The development of a new dose-intensified regimen (BEACOPP) now for the first time has significantly improved the prognosis of these patients. Patients who relapse following radiation therapy alone for early stage HD have satisfactory results with combination chemotherapy and are not considered candidates for high-dose chemotherapy with autologous stem cell transplantation. For patients with relapsed HD after combination chemotherapy, the current data support the use of high-dose chemotherapy with autologous stem cell transplantation.
Inhibition of porcupine prolongs metastasis free survival in a mouse xenograft model of Ewing sarcoma

The most pressing unmet clinical need for patients with Ewing sarcoma (ES) is the prevention and treatment of metastasis. The Wnt signaling pathway regulates a number of cellular functions associated with metastasis, including proliferation, motility, and stem cell self-renewal. Functional interaction between Wnt ligands and their receptors requires palmitoylation by Porcupine (Porcn), making this an ideal therapeutic target. We studied the effect of WNT974, a potent, selective Porcn inhibitor, on ES metastasis. In vitro, WNT974 does not affect ES proliferation or sarcosphere formation, but suppresses multiple transcriptional regulators of metastasis and inhibits cell migration. In vivo, in an orthotopic implantation/amputation model of spontaneous distant metastasis, single agent WNT974 treatment leads to a significant delay in formation of lung metastasis and a substantial improvement in post-amputation survival without a major effect on primary tumor growth. The drug produces no survival benefit in a tail vein injection model, supporting the hypothesis that WNT974 inhibits early steps in the metastatic cascade, such as migration and invasion. Our findings strongly implicate Wnt signaling in the early steps of ES metastasis and demonstrate that WNT974 has the potential to significantly improve the survival of ES patients through the specific inhibition of metastasis.
Electrocardiographic T Wave and its Relation With Ventricular Repolarization Along Major Anatomical Axes

Background—The genesis of the electrocardiographic T wave is incompletely understood and subject to controversy. We have correlated the ventricular repolarization sequence with simultaneously recorded T waves. Methods and Results—Nine pig hearts were Langendorff-perfused (atrial pacing, cycle length 650 ms). Local activation and repolarization times were derived from unipolar electrograms sampling the ventricular myocardium. Dispersion of repolarization time was determined along 4 anatomic axes: left ventricle (LV)–right ventricle (RV), LV:apico-basal, LV:anterior-posterior, and LV:transmural. The heart was immersed in a fluid-filled bucket containing 61 electrodes to determine Tp (Tpeak in lead of maximum integral), TpTe (Tp to Tend), and TpTe_total (first Tpeak in any lead to last Tend in any lead). Repolarization was nonlinearly distributed in time. RT25 (time at which 25% of sites were repolarized, 288±26 ms) concurred with Tp. TpTe was 38±8 ms, and TpTe_total was 75±9 ms. TpTe_total correlated with dispersion of repolarization time in the entire heart (73±18 ms), but not with dispersion of repolarization times along individual axes (LV–RV, 66±17 ms; LV:apico-basal, 51±18 ms; LV:anterior-posterior, 51±27 ms; mean LV:transmural, 14±7 ms; all n=9). Conclusions—We provide a correlation between local repolarization and T wave in a pseudo-ECG. Repolarization differences along all anatomic axes contribute to the T wave. TpTe_total represents total dispersion of repolarization. At Tp, ≈25% of ventricular sites have been repolarized.
SNR-Based Progressive Learning of Deep Neural Network for Speech Enhancement

In this paper, we propose a novel progressive learning (PL) framework for deep neural network (DNN) based speech enhancement. It aims at decomposing the complicated regression problem of mapping noisy to clean speech into a series of subproblems for enhancing system performances and reducing model complexities. As an illustration, we design a signal-tonoise ratio (SNR) based PL architecture by guiding each hidden layer of the DNN to learn an intermediate target with gradual SNR gains explicitly. Furthermore, post-processing, with the rich set of information from the multiple learning targets, can further be conducted. Experimental results demonstrate that SNRbased progressive learning can effectively improve perceptual evaluation of speech quality and short-time objective intelligibility in low SNR environments, and reduce the model parameters by 50% when compared with the DNN baseline system. Moreover, when combined with post-processing, the proposed approach can be further improved.
Strategies for Retaining Midcareer Nurses

One method of reducing predicted shortages because of the aging nursing workforce is to increase retention. Few studies have examined the unique needs of midcareer nurses. A mixed-method approach including surveys and focus groups was used to identify key retention strategies and desires for midcareer nurses. Salary, benefits, positive working relationships, flexible scheduling, and the opportunity for continued education were identified as key retention strategies from this study. Registered nurses in this study reported higher perceptions of their work and work environment than licensed practical nurses did. Differences in work outcomes were evident across sectors, with community nurses reporting higher levels of job satisfaction and perceptions of work quality than nurses in acute and long-term care. Findings suggest that recruitment opportunities may exist with midcareer nurses seeking employment to return to work after time off to have a family. Proactive retention policies that focus on the needs of midcareer nurses would demonstrate a commitment and interest in keeping them in their work positions and in the profession.
A Remote Vision Guidance System for Visually Impaired Pedestrians

This paper presents research and development work on a novel system with a view of developing a navigation system for the guidance of visually impaired pedestrians. The prime aim of the new developed system is to enhance the mobility of visually impaired pedestrians using remote guidance provided by sighted person. However, the system can be used in many other applications. The system implementation is based on the integration of the Global Positioning System (GPS), Geographical Information System (GIS) database and a remote vision facility over the third generation (3G) of mobile networks, providing a technological platform enabling visually impaired pedestrians to be guided remotely by a sighted guide.
Thyroid Ultrasound Findings 7 Years after the Chernobyl Accident

Aims: The accident at the Chernobyl nuclear power station occurred in April 1986. We report on a comparative epidemiological study on thyroid abnormalities in the contaminated and uncontaminated populations of the Bryansk region, South-West Russia, in 1993, 7 years after the accident. Material and Methods: The study material consisted of all inhabitants aged 3–34 years in the contaminated village of Mirnyi and in the uncontaminated village of Krasnyi Rog, excluding those who had moved to the villages after the accident. The total material comprised 302 inhabitants in Mirnyi and 200 in Krasnyi Rog. Results: No pathological US findings in either village were found in children born after the accident. In the age group 0–9 years old at the time of the accident, the prevalence of thyroid abnormalities was 8.1% in the contaminated village compared to 1.6% in the uncontaminated village. In the age group 10–27 years the corresponding figures were 18.8% and 17.7%. Only 55% of the pathological US findings were detected by physical palpation. Conclusion: The total prevalence of thyroid abnormalities was higher among children in the contaminated village. We recommend an active screening of young contaminated subjects with US, supplemented with fine needle biopsy.
Attribute transformations for data mining I: Theoretical explorations

Attribute (feature) transformations on databases are examined from a data mining prospect. Theoretical examples from classical mathematics are used to illustrate the effects of the transformations: (1) Certain examples show that attribute transformations are the only means to bring out the patterns to visible states. (2) There are no apparent hints from the raw data as to what transformations could be employed; domain experts need to be in the loop of data mining. (3) All transformations can be expressed, or more precisely approximated, by polynomials. Such expressions provide some means for a brute force search (one degree at a time) of the transformations. A reasonable success in a linear case (degree one) is reported in Ref. 2 . © 2002 John Wiley & Sons, Inc.
Interval and continuous training are similarly effective in chronic obstructive pulmonary disease

1. Beauchamp MK, 2. Nonoyama M, 3. Goldstein RS, 4. et al . Thorax, 2010;65:157–64. [OpenUrl][1][Abstract/FREE Full Text][2] People with chronic obstructive pulmonary disease (COPD) experience progressive airflow limitation and are predisposed to respiratory infections, both of which can limit their exercise capacity, and quality and length of life. People with COPD benefit from pulmonary rehabilitation, which involves exercise training, education and psychosocial support. Exercise training does not improve lung function but instead reverses deconditioning and maximises the available exercise capacity to reduce the impact of COPD. Increasing the intensity of training results in greater gains in exercise capacity, but many people with COPD are unable to sustain high-intensity training. An alternative to continuous exercise is interval training, which involves periods of high-intensity exercise separated by recovery periods. Interval training may provide a tolerable training regimen with a greater overall training load than continuous exercise. This systematic review by Beauchamp and colleagues aimed to synthesise the best available evidence comparing the effectiveness of continuous and interval exercise training on exercise capacity and health-related quality of life in people with COPD. Six key biomedical databases were searched for appropriate studies published up until May 2009. The reference lists of identified studies were hand-searched. Only randomised trials of continuous versus interval exercise training on a cycle ergometer or treadmill were included. Participants had to have a clinical diagnosis of COPD, with impairment of either the forced expiratory volume in one second (FEV … [1]: {openurl}? query=rft.jtitle%253DThorax%26rft_id%253Dinfo%253Adoi%252F10.1136%252Fthx.2009. 123000%26rft_id%253Dinfo%253Apmid%252F19996334%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [2]: /lookup/ijlink? linkType=ABST&journalCode=thoraxjnl&resid=65/2/157&atom=%2Fbjsports%2F45%2F2%2F155.atom
Finding a Location for a New Word in WordNet

FinnWordNet is a Finnish wordnet which complies with the structure of the Princeton WordNet (Fellbaum, 1998). It was created by translating all the words in Princeton WordNet. It is open source and contains over 117 000 synsets. We are now testing different methods in order to improve and expand the content of FinnWordNet. Since wordnets are structured ontologies, a location for a word in FinnWordNet can be pinpointed by its relations to other words. To us, finding a location for a word therefore means finding a hyperonym, a hyponym or a synonym for the word. This article describes some methods for finding a location for a new word in FinnWordNet. Our methods include searching for multiword terms, compounds and lexicosyntactic patterns. Testing shows that with a few simple methods, we were able to find an indicator of the location for 83.2 % of new words. Out of the new synonym pairs we tested, we were able to find an indication for 86.7 %.
PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers

MOTIVATION Huge genetic datasets with dense marker panels are now common. With the availability of sequence data and recognition of importance of rare variants, smaller studies based on pedigrees are again also common. Pedigree-based samples often start with a dense marker panel, a subset of which may be used for linkage analysis to reduce computational burden and to limit linkage disequilibrium between single-nucleotide polymorphisms (SNPs). Programs attempting to select markers for linkage panels exist but lack flexibility. RESULTS We developed a pedigree-based analysis pipeline (PBAP) suite of programs geared towards SNPs and sequence data. PBAP performs quality control, marker selection and file preparation. PBAP sets up files for MORGAN, which can handle analyses for small and large pedigrees, typically human, and results can be used with other programs and for downstream analyses. We evaluate and illustrate its features with two real datasets. AVAILABILITY AND IMPLEMENTATION PBAP scripts may be downloaded from http://faculty.washington. edu/wijsman/software.shtml. CONTACT wijsman@uw.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Anterior tongue cancer with no history of tobacco and alcohol use may be a distinct molecular and clinical entity.

BACKGROUND A small, albeit significant, number of head and neck squamous cell carcinoma (HNSCC) patients has no history of tobacco and alcohol use. Such non-habits associated HNSCCs may represent a distinct clinical entity and exhibit increased aggressiveness. The objective of the study was to understand differences in molecular etiology of habits, and non-habits associated tongue carcinomas. MATERIALS AND METHODS High-throughput gene expression profiling of 22 tumor samples was carried out. This was followed by quantitative real-time PCR validation of four of the identified differentially expressed genes. RESULTS AND CONCLUSION Eighteen genes were identified that correlate strongly with the habits- and non-habits distinction. Among the genes significantly overexpressed in the non-habits group are CCND1, a key cell-cycle regulator, DACT3, a modulator of the Wnt/beta-catenin pathway, and three genes associated with the Notch signaling pathway. CCND1 and DACT3 overexpression in non-habits associated tongue carcinomas were subsequently validated by quantitative real-time PCR in an independent cohort (n = 18) of patient samples. Gene expression data were integrated with publicly available protein interaction data to build a small protein interaction network containing five of 18 differentially expressed genes. This suggested that a functional 'network module' can be implicated in the subgroup distinction. All the tumors analyzed here were human papillomavirus (HPV) negative samples. An association between CCND1 overexpression in oral tumors and poor prognosis has previously been reported. Thus, CCND1 overexpression in non-habits associated anterior tongue carcinomas may contribute to their increased clinical aggressiveness.
Crystal structure and DFT study of (E)-2-chloro-4-{[2-(2,4-dinitrophenyl)hydrazin-1-ylidene]methyl}phenol acetonitrile hemisolvate

The title Schiff base compound was obtained from a condensation reaction of 4-chloro-3-hydroxybenzaldehyde and 2,4-dinitrophenylhydrazine. The molecule is almost planar with the dihedral angle between the benzene rings being 3.70 (17)°.
EFFECT OF BODY POSITION DURING WHOLE BODY VIBRATION ON ACUTE JUMPING PERFORMANCE

Background. The aim of the study was to investigate the acute effect of whole-body vibration (WBV) during heel raised and standing squat position on squat (SJ) and countermovement jump (CMJ) heights. Methods. Twenty four physically active sport science students are voluntarily participated in this study. Randomized, counterbalanced, crossover study was used in this study and all subjects completed two trials that were plantar (25–30°) and dorsal (5–10°) flexion squats. WBV exercises were performed on a vibration plate at 26 Hz frequency, 4mm amplitude. Jumping performances were assessed with and without WBV conditions. Subjects executed WBV condition treatment on static plantar or dorsal flexion half squat position (45°knee angle) for 3x60 s with 60 s rest between sets. Results. There was no statistically significant two-way interaction between treatments and times for SJ and CMJ (p > .05). SJ and CMJ after the WBV were significantly higher than without WBV condition (p < .05). SJ and CMJ heights were higher than baseline values without WBV. Conclusion. These results indicate that there were no differences between WBV during plantar and dorsal flexion squat position on SJ and CMJ heights. Regardless of different muscle length squat position during WBV, there were little but significant differences (~1cm) on SJ and CMJ heights after WBV. According to these results it can be said that WBV had a statistically significant acute effect on jumping, but different plantar-flexor muscle length squat position on vibration plate during WBV did not have any effect on jumping performance.
The Bolocam Galactic Plane Survey: II. Catalog of The Image Data

We present a catalog of 8358 sources extracted from images produced by the Bolocam Galactic Plane Survey (BGPS). The BGPS is a survey of the millimeter dust continuum emission from the northern Galactic plane. The catalog sources are extracted using a custom algorithm, Bolocat, which was designed speciﬁcally to identify and characterize objects in the large-area maps generated from the Bolocam instrument. The catalog products are designed to facilitate follow-up observations of these relatively unstudied objects. The catalog is 98% complete from 0.4 Jy to 60 Jy over all object sizes for which the survey is sensitive ( < 3 . (cid:3) 5). We ﬁnd that the sources extracted can best be described as molecular clumps—large dense regions in molecular clouds linked to cluster formation. We ﬁnd that the ﬂux density distribution of sources follows a power law with dN/dS ∝ S − 2 . 4 ± 0 . 1 and that the mean Galactic latitude for sources is signiﬁcantly below the midplane: (cid:5) b (cid:6) = ( − 0 . ◦ 095 ± 0 . ◦ 001).
Meaningful Adoption: What We Know or Think We Know About the Financing, Effectiveness, Quality, and Safety of Electronic Medical Records

As ONC is working hard to draft the final regulations for Stage 2 of Meaningful Use (MU), its policy teams are working on the framework for Stage 3. Although the stimulus program has several more years to run early adopters who sought to maximize their receipt of federal funding will soon be reaching the mid-point of their journey. As a result data points are now emerging for some of the more important features of the program’s implementation. These data points can be compared to expectations set both in 2009 and earlier. This article reviews the history of MU and examines the level of current and projected implementation. It challenges the basis for some of the positive cheerleading surrounding the subsidy program and questions the quality of the installed base of EMRs. The critical analysis then extends outside of compliance with the quality and effectiveness requirements of MU to safety externalities and their regulatory and liability implications.
SOME THOUGHTS ON INTERFACE STRUCTURE ( S )

There has recently been a very interesting public exchange of views regarding the relationship between MT and linguistics (Kettunen 1986; Slocum 1986). Kettunen – responding to Slocum's (1985) article – criticises MT for the fact that it sacrifices its reliance on "linguistically sound principles" to the goal of producing acceptable translations cost-effectively. For this reason, "the results may not have much to say to computational linguistics or to linguistics proper. " Slocum's reply is that to a great extent "linguistic theory fails to account for linguistic fact", that "MT system developers have less time to engage in theorizing than they might like", and that "theoretical linguists (.) seldom if ever engage in application development".