Miracle-dz/UniFAR-FTUs huggingface dataset:
Frequency of enterovirus detection in blood samples of neonates admitted to hospital with sepsis‐like illness in Kuwait

This study investigated the role of enteroviruses in sepsis‐like illness among neonates in Kuwait. Serum samples from 139 consecutive neonates presenting with sepsis‐like illness during a three and a half‐year‐period whose blood cultures were negative for bacterial pathogens were tested. Enterovirus RNA was detected by single‐step reverse‐transcription PCR (RT‐PCR). Specific genotypes were identified by direct DNA sequencing of enteroviral genome. Serotype‐specific antibodies in serum samples from some selected patients were detected by virus neutralization test using coxsackievirus B types (CBVs). All 139 neonates presented with sepsis‐like illness and blood samples were uniformly negative for aerobic/anaerobic bacterial cultures. Fifty‐six (40%) neonates had further complications of sepsis including carditis (n = 34) and multi‐organ involvement (n = 22). Enterovirus RNA was detected by RT‐PCR in 34 of 139 (24%) serum samples which is among the highest frequency reported so far in non‐epidemic settings. Genotyping identified CBVs as most common enteroviruses, causing 19 of 34 (56%) enteroviral sepsis episodes in neonates. Of 34 carditis cases, 18 were positive for CBVs by serotyping including all 10 enterovirus RNA‐positive samples. Only one fatality was observed due to liver failure in a neonate with hepatitis. Our data showed that enteroviruses are responsible for 24% of neonatal sepsis cases due to non‐bacterial causes in Kuwait. The data indicate that enteroviruses should be considered in the differential diagnosis of sepsis‐like illness among neonates, particularly those with negative blood cultures for bacterial pathogens. J. Med. Virol. 85:1280–1285, 2013. © 2013 Wiley Periodicals, Inc.
Health-related quality of life in recurrent platinum-sensitive ovarian cancer--results from the CALYPSO trial.

BACKGROUND In the CALYPSO trial, carboplatin-pegylated liposomal doxorubicin (CD) demonstrated superior therapeutic index versus carboplatin-paclitaxel (CP) in patients with recurrent ovarian cancer. This paper reports the health-related quality of life (HRQoL) findings. MATERIALS AND METHODS HRQoL was measured with the EORTC QoL-QC30 questionnaire and OV28 ovarian cancer module. Mean change scores from baseline in HRQoL subscales (five functional scales and global health status) in each arm and the proportion of patients improved or worsened were calculated every 3 months until 12 months. RESULTS Compliance was 90% at baseline and 76%, 64%, 57% at 3, 6, and 9 months, respectively. Baseline HRQoL showed already impaired global scores (mean 62/100) and considerable symptom burden (90% of patients reporting nonzero scores). Global QoL and abdominal symptom scores improved over time in both arms; at 6 months, 36% of patients met criteria for improved symptoms. Treatment with CD resulted in less peripheral neuropathy (9.8 versus 24.2), fewer other chemotherapy side-effects (9.5 versus 16.2), and less impact on body image (3.8 versus 10.4) versus CP (all P<0.02) at 6 months. CONCLUSIONS These patient-reported outcomes confirm the overall lower toxicity of CD versus CP. The improved disease-related outcomes achieved with CD were not at the expense of QoL.
Graph-Based Blind Image Deblurring From a Single Photograph

Blind image deblurring, i.e., deblurring without knowledge of the blur kernel, is a highly ill-posed problem. The problem can be solved in two parts: 1) estimate a blur kernel from the blurry image, and 2) given an estimated blur kernel, de-convolve the blurry input to restore the target image. In this paper, we propose a graph-based blind image deblurring algorithm by interpreting an image patch as a signal on a weighted graph. Specifically, we first argue that a skeleton image—a proxy that retains the strong gradients of the target but smooths out the details—can be used to accurately estimate the blur kernel and has a unique bi-modal edge weight distribution. Then, we design a reweighted graph total variation (RGTV) prior that can efficiently promote a bi-modal edge weight distribution given a blurry patch. Further, to analyze RGTV in the graph frequency domain, we introduce a new weight function to represent RGTV as a graph $l_{1}$ -Laplacian regularizer. This leads to a graph spectral filtering interpretation of the prior with desirable properties, including robustness to noise and blur, strong piecewise smooth filtering, and sharpness promotion. Minimizing a blind image deblurring objective with RGTV results in a non-convex non-differentiable optimization problem. Leveraging the new graph spectral interpretation for RGTV, we design an efficient algorithm that solves for the skeleton image and the blur kernel alternately. Specifically for Gaussian blur, we propose a further speedup strategy for blind Gaussian deblurring using accelerated graph spectral filtering. Finally, with the computed blur kernel, recent non-blind image deblurring algorithms can be applied to restore the target image. Experimental results demonstrate that our algorithm successfully restores latent sharp images and outperforms the state-of-the-art methods quantitatively and qualitatively.
On the massive stellar population of the super star cluster Westerlund 1

We present new spectroscopic and photometric observations of the young Galactic open cluster Westerlund 1 (Wd 1) that reveal a unique population of massive evolved stars. We identify ∼200 cluster members and present spectroscopic clas- sifications for ∼25% of these. We find that all stars so classified are unambiguously post-Main Sequence objects, consistent with an apparent lack of an identifiable Main Sequence in our photometric data to V ∼ 20. We are able to identify rich popu- lations of Wolf Rayet stars, OB supergiants and short lived transitional objects. Of these, the latter group consists of both hot (Luminous Blue Variable and extreme B supergiant) and cool (Yellow Hypergiant and Red Supergiant) objects - we find that half the known Galactic population of YHGs resides within Wd 1. We obtain a mean V − MV ∼ 25 mag from the cluster Yellow Hypergiants, implying a Main Sequence turnoff at or below MV = −5 (O7 V or later). Based solely on the masses inferred for the 53 spectroscopically classified stars, we determine an absolute minimum mass of ∼1.5 × 10 3 Mfor Wd 1. However, considering the complete photometrically and spectroscopically selected cluster population and adopting a Kroupa IMF we infer a likely mass for Wd 1 of ∼10 5 M� , noting that inevitable source confusion and incompleteness are likely to render this an underestimate. As such, Wd 1 is the most massive compact young cluster yet identified in the Local Group, with a mass exceeding that of Galactic Centre clusters such as the Arches and Quintuplet. Indeed, the luminosity, inferred mass and com- pact nature of Wd 1 are comparable with those of Super Star Clusters - previously identified only in external galaxies - and is consistent with expectations for a Globular Cluster progenitor.
Extensive Evolution of Cereal Ribosome-Inactivating Proteins Translates into Unique Structural Features, Activation Mechanisms, and Physiological Roles

Ribosome-inactivating proteins (RIPs) are a class of cytotoxic enzymes that can depurinate rRNAs thereby inhibiting protein translation. Although these proteins have also been detected in bacteria, fungi, and even some insects, they are especially prevalent in the plant kingdom. This review focuses on the RIPs from cereals. Studies on the taxonomical distribution and evolution of plant RIPs suggest that cereal RIPs have evolved at an enhanced rate giving rise to a large and heterogeneous RIP gene family. Furthermore, several cereal RIP genes are characterized by a unique domain architecture and the lack of a signal peptide. This advanced evolution of cereal RIPs translates into distinct structures, activation mechanisms, and physiological roles. Several cereal RIPs are characterized by activation mechanisms that include the proteolytic removal of internal peptides from the N-glycosidase domain, a feature not documented for non-cereal RIPs. Besides their role in defense against pathogenic fungi or herbivorous insects, cereal RIPs are also involved in endogenous functions such as adaptation to abiotic stress, storage, induction of senescence, and reprogramming of the translational machinery. The unique properties of cereal RIPs are discussed in this review paper.
Barriers and Facilitators toward HIV Testing and Health Perceptions among African-American Men Who Have Sex with Women at a South Side Chicago Community Health Center: A Pilot Study

In the United States, African-Americans’ (AAs) HIV infection rates are higher than any other racial group, and AA men who have sex with women (MSW) are a significant proportion of new cases. There is little research into AA MSW HIV/AIDS knowledge, barriers, and facilitators of HIV testing in Chicago. We enrolled a convenience sample of AA MSW from a community health clinic who completed self-administered surveys assessing HIV knowledge and testing-related barriers and facilitators. The survey was a combination of questions from several validated instruments, and additional questions were written based on key informant interviews with social scientists to tailor the questionnaire for AA men living on the South Side of Chicago. We recruited 20 AA MSW (mean age 47.4 years). Sixty-five percent had incomes <$10,000/year, 30% were insured, and 50% had post-secondary education. Despite low socioeconomic status, their HIV literacy was relatively high. The identified major barriers to testing were low perceived HIV risk, concerns over privacy, and external stigma at testing sites. Future efforts should focus on educating AA MSW on actual risk for HIV and address issues of privacy and stigma at testing sites.
Altered molecular pathways in melanocytic lesions

To identify gene expression changes in melanocytic lesions, biopsies from 18 common nevi (CMN), 11 dysplastic nevi (DN), 8 radial and 15 vertical growth phase melanomas (RGPM, VGPM), and 5 melanoma metastases (MTS) were analyzed using whole genome microarrays. The comparison between CMN and RGPM showed an enrichment of Gene Ontology terms related to inter and intracellular junctions, whereas the transition from RGPM to VGPM underlined the alteration of apoptosis. Upregulation of genes involved in dsDNA break repair and downregulation of cellular adhesion genes were observed in MTS with respect to VGPM. DN exhibited rather heterogeneous molecular profiles, with some proliferation genes expressed at higher levels than in CMN, altered regulation of transcription compared to RGPM and a subset of processes, such as mismatch repair, equally expressed as in VGPM. Furthermore, the expression profile of genes involved into cellular detoxification and antigen presentation split them into two classes, with different proliferation potential. Finally, molecular profiling of individual lesions identified altered biological processes, such as regulation of apoptosis, regulation of transcription and T‐cell activation, not associated with specific histological classes but rather with subgroups of samples without apparent relationship. This holds true for dysplastic nevi in particular. Our data indicate that generally the intersection between stage specific and sample specific molecular alterations may lead to a more precise determination of the individual progression risk of melanocytic lesions.
Learning Adversarially Fair and Transferable Representations

In this paper, we advocate for representation learning as the key to mitigating unfair prediction outcomes downstream. Motivated by a scenario where learned representations are used by third parties with unknown objectives, we propose and explore adversarial representation learning as a natural method of ensuring those parties act fairly. We connect group fairness (demographic parity, equalized odds, and equal opportunity) to different adversarial objectives. Through worst-case theoretical guarantees and experimental validation, we show that the choice of this objective is crucial to fair prediction. Furthermore, we present the first in-depth experimental demonstration of fair transfer learning and demonstrate empirically that our learned representations admit fair predictions on new tasks while maintaining utility, an essential goal of fair representation learning.
Comparison between disease onset patterns of Egyptian juvenile and adult systemic lupus erythematosus (single centre experience)

Background Systemic lupus erythematosus (SLE) is a complex autoimmune disease that occurs worldwide in both children and adults, with different disease manifestations, activity and severity between them. Objectives To analyse the difference in disease onset patterns and activity in Egyptian children and adults with SLE. Methods A retrospective cohort study conducted on 298 Egyptian SLE patients, 215 adults (a-SLE) (>18 years) and 83 children (j-SLE) (≤18 years). Disease onset, clinical manifestations and laboratory investigations were recorded. The systemic lupus erythematosus disease activity index (SLEDAI) was used to assess disease onset activity; renal biopsy was performed for all cases affected with renal symptoms. Results A total of 215 a-SLE (F/M: 14.4/1), mean age 29.65 ± 10.235 years, and 83 j-SLE (F/M: 5.4/1), mean age at diagnosis 12.63 ± 3.112 years. The most frequent initial a-SLE symptoms were constitutional (88.8%), mucocutaneous (71.2%), haematological (64.2%), articular (62.3%), renal (43.7%), vascular (15.3%), serositis (14.4%) and finally central nervous system (11.6%). There were no significant differences between a-SLE and j-SLE with regard to constitutional, mucocutaneous, renal, vascular and serositis manifestations, which were 92.8%, 74.7%, 53%, 16.9% and 10.8%, respectively, but the j-SLE haematological (88%) and central nervous system (30.1%) manifestations were significantly higher than a-SLE and articular manifestations were significantly lower in j-SLE (14.5%) than a-SLE. Antinuclear antibodies were positive for 95.3% of a-SLE and 97.6% of j-SLE. Anti-dsDNA was positive for 84.7% a-SLE and was significantly higher in j-SLE (92.8%). The SLEDAI score was 12.23 ± 4.966 in a-SLE and was significantly higher in j-SLE (27.13 ± 19.968). International Society of Nephrology lupus nephritis classes III and IV (42.4%) were the commonest findings in a-SLE; however, classes I and III (57.9%) were the commonest in j-SLE. Conclusions SLE had a wide variety of clinical and immunological manifestations, with some similarity and differences between a-SLE and j-SLE; juvenile onset lupus had a higher SLEDAI with more aggressive initial manifestations than a-SLE.
Trypanocidal and leishmanicidal activities of flavonoids isolated from Stevia satureiifolia var. satureiifolia

Abstract Context Chagas’ disease and leishmaniasis produce significant disability and mortality with great social and economic impact. The genus Stevia (Asteraceae) is a potential source of antiprotozoal compounds. Objective Aerial parts of four Stevia species were screened on Trypanosoma cruzi. Stevia satureiifolia (Lam.) Sch. Bip. var. satureiifolia (Asteraceae) dichloromethane extract was selected for a bioassay-guided fractionation in order to isolate its active compounds. Additionally, the antileishmanial activity and the cytotoxicity of these compounds on mammalian cells were assessed. Materials and methods The dichloromethane extract was fractionated by column chromatography. The isolated compounds were evaluated using concentrations of 0–100 μg/mL on T. cruzi epimastigotes and on Leishmania braziliensis promastigotes for 72 h, on trypomastigotes and amastigotes of T. cruzi for 24 h and 120 h, respectively. The compounds’ cytotoxicity (12.5–500 μg/mL) was assessed on Vero cells by the MTT assay. The structure elucidation of each compound was performed by spectroscopic methods and HPLC analysis. Results The dichloromethane extracts of Stevia species showed significant activity on T. cruzi epimastigotes. The flavonoids eupatorin (1.3%), cirsimaritin (1.9%) and 5-desmethylsinensetin (1.5%) were isolated from S. satureiifolia var. satureiifolia extract. Eupatorin and 5-desmethylsinensetin showed IC50 values of 0.2 and 0.4 μg/mL on T. cruzi epimastigotes and 61.8 and 75.1 μg/mL on trypomastigotes, respectively. The flavonoid 5-desmethylsinensetin showed moderate activity against T. cruzi amastigotes (IC50 value = 78.7 μg/mL) and was the most active compound on L. braziliensis promastigotes (IC50 value = 37.0 μg/mL). Neither of the flavonoids showed cytotoxicity on Vero cells, up to a concentration of 500 μg/mL.
Rethinking the Cognitive Mechanisms Underlying Pantomime of Tool Use: Evidence from Alzheimer’s Disease and Semantic Dementia

Abstract Objectives: Pantomiming the use of familiar tools is a central test in the assessment of apraxia. However, surprisingly, the nature of the underlying cognitive mechanisms remains an unresolved issue. The aim of this study is to shed a new light on this issue by exploring the role of functional, mechanical, and manipulation knowledge in patients with Alzheimer’s disease and semantic dementia and apraxia of tool use. Methods: We performed multiple regression analyses with the global performance and the nature of errors (i.e., production and conception) made during a pantomime of tool use task in patients and control participants as dependent variables and tasks investigating functional, mechanical, and manipulation knowledge as predictors. Results: We found that mechanical problem solving, assessing mechanical knowledge, was a good predictor of the global performance of pantomime of tool use. We also found that occurrence of conception errors was robustly predicted by the task assessing functional knowledge whereas that of production errors was not explained by only one predictor. Conclusions: Our results suggest that both functional and mechanical knowledge are important to pantomime the use of tools. To our knowledge, this is the first demonstration that mechanical knowledge plays a role in pantomime of tool use. Although impairment in pantomime of tool use tasks (i.e., apraxia) is widely explained by the disruption of manipulation knowledge, we propose that pantomime of tool use is a complex problem-solving task. (JINS, 2017, 23, 128–138)
Comparison of 68Ga-DOTA-Siglec-9 and 18F-Fluorodeoxyribose-Siglec-9: Inflammation Imaging and Radiation Dosimetry

Sialic acid-binding immunoglobulin-like lectin 9 (Siglec-9) is a ligand of inflammation-inducible vascular adhesion protein-1 (VAP-1). We compared 68Ga-DOTA- and 18F-fluorodeoxyribose- (FDR-) labeled Siglec-9 motif peptides for PET imaging of inflammation. Methods. Firstly, we examined 68Ga-DOTA-Siglec-9 and 18F-FDR-Siglec-9 in rats with skin/muscle inflammation. We then studied 18F-FDR-Siglec-9 for the detection of inflamed atherosclerotic plaques in mice and compared it with previous 68Ga-DOTA-Siglec-9 results. Lastly, we estimated human radiation dosimetry from the rat data. Results. In rats, 68Ga-DOTA-Siglec-9 (SUV, 0.88 ± 0.087) and 18F-FDR-Siglec-9 (SUV, 0.77 ± 0.22) showed comparable (P = 0.29) imaging of inflammation. In atherosclerotic mice, 18F-FDR-Siglec-9 detected inflamed plaques with a target-to-background ratio (1.6 ± 0.078) similar to previously tested 68Ga-DOTA-Siglec-9 (P = 0.35). Human effective dose estimates for 68Ga-DOTA-Siglec-9 and 18F-FDR-Siglec-9 were 0.024 and 0.022 mSv/MBq, respectively. Conclusion. Both tracers are suitable for PET imaging of inflammation. The easier production and lower cost of 68Ga-DOTA-Siglec-9 present advantages over 18F-FDR-Siglec-9, indicating it as a primary choice for clinical studies.
Stabilization of Isolated Vortices in a Rotating Stratified Fluid

The key element of Geophysical Fluid Dynamics—reorganization of potential vorticity (PV) by nonlinear processes—is studied numerically for isolated vortices in a uniform environment. Many theoretical studies and laboratory experiments suggest that axisymmetric vortices with a Gaussian shape are not able to remain circular owing to the growth of small perturbations in the typical parameter range of abundant long-lived vortices. An example of vortex destabilization and the eventual formation of more intense self-propagating structures is presented using a 3D rotating stratified Boussinesq numerical model. The peak vorticity growth found during the stages of strong elongation and fragmentation is related to the transfer of available potential energy into kinetic energy of vortices. In order to develop a theoretical model of a stable circular vortex with a small Burger number compatible with observations, we suggest a simple stabilizing procedure involving the modification of peripheral PV gradients. The results have important implications for better understanding of real-ocean eddies.
Long-Term Outcome of Patients Undergoing Minimally Invasive Direct Coronary Artery Bypass Surgery

Objective The primary objective was to investigate the long-term survival of patients who underwent single-vessel coronary revascularization with minimally invasive direct coronary artery bypass surgery with or without hybrid revascularization. The secondary outcome measures were repeat revascularization either by coronary artery bypass grafting or by percutaneous coronary intervention and the incidence of myocardial infarction or recurrent angina. Methods This is a retrospective study of prospectively collected data of patients who underwent minimally invasive direct coronary artery bypass procedure in our center between January 2001 and December 2015. Procedures were performed either through small left anterolateral thoracotomy or lower midline sternotomy. Results A total of 182 patients were identified: 100 underwent minimally invasive direct coronary artery bypass to the left anterior descending artery and 82 underwent hybrid revascularization (percutaneous coronary intervention to coronary arteries other than the left anterior descending artery along with minimally invasive direct coronary artery bypass to the left anterior descending artery). The mean ± SD age was 62 ± 10.1 years. Preoperatively 82% were male, and 72.5% patients had good left ventricular function. The median follow-up period was 10.9 years. There was no inhospital or 30-day mortality. The 10-year actuarial survival was 84.8%. Freedom from repeat revascularization was 98.9% at 1 year and 89.9% at 10 years. At follow-up, freedom from myocardial infarction was 96.7% whereas freedom from angina was 92.9%. Conclusions Within the limitations imposed by retrospective analyses, our study demonstrates excellent long-term outcome in patients undergoing minimally invasive direct coronary artery bypass with or without hybrid revascularization. For isolated left anterior descending artery disease minimally invasive direct coronary artery bypass should be considered, whereas hybrid revascularization (percutaneous coronary intervention and minimally invasive direct coronary artery bypass) should be considered for multivessel disease.