Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Human Monoclonal Antibody 80R for Immunoprophylaxis of Severe Acute Respiratory Syndrome by an Animal Study, Epitope Mapping, and Analysis of Spike Variants

ABSTRACT In this report, the antiviral activity of 80R immunoglobulin G1 (IgG1), a human monoclonal antibody against severe acute respiratory syndrome coronavirus (SARS-CoV) spike (S) protein that acts as a viral entry inhibitor in vitro, was investigated in vivo in a mouse model. When 80R IgG1 was given prophylactically to mice at doses therapeutically achievable in humans, viral replication was reduced by more than 4 orders of magnitude to below assay limits. The essential core region of S protein required for 80R binding was identified as a conformationally sensitive fragment (residues 324 to 503) that overlaps the receptor ACE2-binding domain. Amino acids critical for 80R binding were identified. In addition, the effects of various 80R-binding domain amino acid substitutions which occur in SARS-like-CoV from civet cats, and which evolved during the 2002/2003 outbreak and in a 2003/2004 Guangdong index patient, were analyzed. The results demonstrated that the vast majority of SARS-CoVs are sensitive to 80R. We propose that by establishing the susceptibility and resistance profiles of newly emerging SARS-CoVs through early S1 genotyping of the core 180-amino-acid neutralizing epitope of 80R, an effective immunoprophylaxis strategy with 80R should be possible in an outbreak setting. Our study also cautions that for any prophylaxis strategy based on neutralizing antibody responses, whether by passive or active immunization, a genotyping monitor will be necessary for effective use.
A New method for determining cumulative gravitational lensing effects in inhomogeneous universes

We present a new approach to calculating the statistical distributions for magnification, shear, and rotation of images of cosmological sources due to gravitational lensing. In this approach one specifies an underlying Robertson-Walker cosmological model together with relevant information on the clumping of matter on scales much smaller than the Hubble radius. The geodesic deviation equation is then integrated backwards in time until the desired redshift is reached, using a Monte Carlo procedure wherein each photon beam in effect ``creates its own universe'' as it propagates. The approach is somewhat similar to that used in ``Swiss cheese'' models, but the ``cheese'' has been completely eliminated, the matter distribution in the ``voids'' need not be spherically symmetric, and the total mass in each void need equal the corresponding Robertson-Walker mass only on average. We show that when the matter in the universe consists of point masses, the statistical distributions of the lensing images are essentially independent of both the mass spectrum and clustering properties of the point masses, provided that the clustering is spherical. We apply our results (i) to argue that the positive correlation recently found between quasar luminosity and the number of absorption line systems is not likely to be due to lensing, and (ii) to determine the amount of ``noise'' and possible bias produced by lensing in measurements of $q_0$ using distant supernovae.
Fast learning rates for plug-in classifiers

It has been recently shown that, under the margin (or low noise) assumption, there exist classifiers attaining fast rates of convergence of the excess Bayes risk, that is, rates faster than n -1/2 . The work on this subject has suggested the following two conjectures: (i) the best achievable fast rate is of the order n -1 , and (ii) the plug-in classifiers generally converge more slowly than the classifiers based on empirical risk minimization. We show that both conjectures are not correct. In particular, we construct plug-in classifiers that can achieve not only fast, but also super-fast rates, that is, rates faster than n -1 . We establish minimax lower bounds showing that the obtained rates cannot be improved.
Opposing BOLD responses to reciprocated and unreciprocated altruism in putative reward pathways

Mesencephalic dopamine neurons are believed to facilitate reward-dependent learning by computing errors in reward predictions. We used fMRI to test whether this system was activated as expected in response to errors in predictions about whether a social partner would reciprocate an act of altruism. Nineteen subjects received fMRI scans as they played a series of single-shot Prisoner's Dilemma games with partners who were outside the scanner. In both ventromedial prefrontal cortex and ventral striatum, reciprocated and unreciprocated cooperation were associated with positive and negative BOLD responses, respectively. Our results are consistent with the hypothesis that mesencephalic dopamine projection sites carry information about errors in reward prediction that allow us to learn who can and cannot be trusted to reciprocate favors.
Interpolation methods in model predictive control: an overview

Interpolation methods are one means of tackling the classical performance versus feasibility compromise in model predictive control (MPC). However, although some details are available in various conferences, very little has appeared in the published journals and also there is no paper pulling all the various algorithms together. Hence this article seeks to give a brief but insightful survey of existing proposals along with their strengths and weaknesses, before proposing useful avenues for future studies.
On the rate distortion region of Gaussian multiterminal source coding

We consider the distributed source coding system of L correlated Gaussian sources Y<inf>i</inf>, i = 1,2,· · ·, L. We assume that Y<sup>L</sup> = <sup>t</sup>(Y<inf>1</inf>, Y<inf>2</inf>, ···, Y<inf>L</inf>) is an observation of the remote source vector X<sup>L</sup> = <sup>t</sup>(X<inf>1</inf>, X<inf>2</inf>, ···, X<inf>L</inf>), having the form Y <sup>L</sup> = X<sup>K</sup> + N<sup>L</sup>, where N<sup>L</sup> = <sup>t</sup>(N<inf>1</inf>, N<inf>2</inf>, ···, N<inf>L</inf>) is a vector of L independent Gaussian random variables also independent of X<sup>L</sup>. In this system L correlated Gaussian observations are separately compressed by L encoders and sent to the information processing center. In this paper, we study the multiterminal source coding problem where the decoder wishes to reconstruct the observation Y<sup>L</sup> = X<sup>L</sup> +N<sup>L</sup>. We consider three distortion criteria based on the covariance matrix of the estimation error on Y<sup>L</sup>. For each of those three criteria we derive explicit inner and outer bounds of the rate distortion region.
Evolutionary Pressure on Mitochondrial Cytochrome b Is Consistent with a Role of CytbI7T Affecting Longevity during Caloric Restriction

Background Metabolism of energy nutrients by the mitochondrial electron transport chain (ETC) is implicated in the aging process. Polymorphisms in core ETC proteins may have an effect on longevity. Here we investigate the cytochrome b (cytb) polymorphism at amino acid 7 (cytbI7T) that distinguishes human mitochondrial haplogroup H from haplogroup U. Principal Findings We compared longevity of individuals in these two haplogroups during historical extremes of caloric intake. Haplogroup H exhibits significantly increased longevity during historical caloric restriction compared to haplogroup U (p = 0.02) while during caloric abundance they are not different. The historical effects of natural selection on the cytb protein were estimated with the software TreeSAAP using a phylogenetic reconstruction for 107 mammal taxa from all major mammalian lineages using 13 complete protein-coding mitochondrial gene sequences. With this framework, we compared the biochemical shifts produced by cytbI7T with historical evolutionary pressure on and near this polymorphic site throughout mammalian evolution to characterize the role cytbI7T had on the ETC during times of restricted caloric intake. Significance Our results suggest the relationship between caloric restriction and increased longevity in human mitochondrial haplogroup H is determined by cytbI7T which likely enhances the ability of water to replenish the Qi binding site and decreases the time ubisemiquinone is at the Qo site, resulting in a decrease in the average production rate of radical oxygen species (ROS).
Individual differences in behavioral flexibility in a probabilistic reversal learning task : an fMRI study

Behavioral flexibility is an important aspect of self-regulation and involves effectively learning, unlearning, and relearning associations between actions and outcome. Using a probabilistic reversal learning paradigm (PRL), the neural correlates of flexibility have previously been associated with brain regions implicated in cognitive control, including the anterior cingulate cortex (ACC) and lateral prefrontal cortex, and with the nucleus accumbens (Nacc) implicated in reward. The current study on healthy young males (n = 40) extends this previously published work in 3 ways. First we corroborate the involvement of ACC, VLPFC, and DLPFC at the exact moment of behavioral switches. Second, we report increased activation of the dACC and caudate head with increasing number of perseverating errors preceding a behavioral switch. Third, better performance on the task is associated with increased activation of rACC and VLPFC during switching, suggesting that these regions contribute to individual differences in behavioral flexibility. These findings cannot be extended to individual differences in a self-reported measure of self-regulation.
Lymphatic spread of ductal pancreatic adenocarcinoma is independent of lymphangiogenesis

Early lymph node metastasis is common in pancreatic ductal adenocarcinoma (PDAC). The present study has examined the relationship of lymphatic spread to lymph vessel development and the expression of lymphangiogenic cytokines in a series of well‐characterized PDACs. The hot spot method revealed the intratumoural and peritumoural lymphatic vessel density (LVD) to be slightly higher in PDACs than in the normal pancreas. The average intratumoural LVD, however, was strikingly decreased. There was no overexpression of vascular endothelial growth factor (VEGF)‐C and VEGF‐D in PDACs compared with the normal pancreas. LVD and expression of lymphangiogenic cytokines were not related to any of the biological tumour features or to patient survival. Three orthotopic nude mouse PDAC models did not reveal any increase in tumour‐associated LVD, despite a high rate of lymph node metastasis. Lymph vessel proliferation was comparable in PDAC and chronic pancreatitis, in both humans and mice. In conclusion, increased lymphangiogenic activity is not required for and does not significantly affect the lymphatic spread of PDAC. The reduced number of human and murine intratumoural lymph vessels indicates that lymphatic metastasis takes place predominantly via peritumoural lymphatic vessels. The weak expression of lymphangiogenic cytokines in neoplastic cells and lymphatic vessel proliferation in peritumoural regions and chronic pancreatitis indicate that inflammation may be the reason for the low rate of lymphangiogenesis. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Pretreatment serum interleukin-6 concentration as a prognostic factor of overall survival in metastatic malignant melanoma patients treated with biochemotherapy: a retrospective study

Biological response parameters during biochemotherapy, including chemotherapy with immune modulating agents, have been studied extensively. Of these parameters, interleukin-6 (IL-6) has been implicated in advanced stage disease and tumour recurrence. However, there is limited information available about the significance of IL-6 in metastatic malignant melanoma (MMM). In this study, we evaluated the possible relationship between serum IL-6 level and overall survival. This retrospective study included 125 patients with MMM. Pretreatment serum IL-6 levels were determined using a highly sensitive enzyme-linked immunosorbent assay (ELISA) test. Kaplan–Meier survival curves were constructed and compared using the log-rank test. Cox proportional analysis was performed to assess the predictors of overall survival, which was calculated from the beginning of biochemotherapy until death. In order to establish the possible relationship between IL-6 level and overall survival, patients were divided into two groups according to a cut-off of 5 pg/ml, corresponding to the first quartile obtained by descriptive statistics of the pretreatment IL-6 level in all patients. Thirty-five patients were in the low IL-6 group and 76 patients were in the high IL-6 group. Based on this stratification, overall survival was shown to be affected by IL-6 serum level: it was higher (24.6 months) in the low IL-6 group when compared with the high IL-6 group (9.7 months) (P=0.0006). Furthermore, Cox multivariate analysis including standard melanoma prognostic factors showed that IL-6, as a variable, lactate dehydrogenase (LDH) and tumour burden were significant prognostic factors for overall survival. On the basis of this evidence, the pretreatment serum IL-6 level is a predictive factor of overall survival in MMM.
Weight bearing does not contribute to the development of osteonecrosis of the femoral head

The hip joint is one of the major structures in the human body and the resultant force acting through the hip joint is 300% of body weight. Therefore, weight bearing, as a cause of ischaemia, may contribute to the development of non‐traumatic osteonecrosis of the femoral head (ONFH). However, it remains unclear whether weight bearing is related to the development of non‐traumatic ONFH. Therefore the aim of this study was to clarify the role of weight bearing in the development of non‐traumatic ONFH. Non‐weight‐bearing (NWB) rats were tail suspended to prevent any weight coming to bear on the hindlimbs from day 1 to the time of sacrifice. The weight‐bearing (WB) group rats were also housed individually, although without tail suspension. All rats were injected with lipopolysaccharide and methylprednisolone to promote the development of non‐traumatic ONFH. All animals were sacrificed three weeks after the final methylprednisolone injection. Histopathological analysis was performed. Osteonecrosis of the femoral head was observed not only in the NWB but also in the WB rats; however, no osteonecrosis of the humeral head was observed in either group. We confirmed that non‐traumatic ONFH developed in NWB rats, suggesting that weight bearing does not contribute to the development of non‐traumatic ONFH in rats.
Surface Nucleation Comment Comment on Evidence for Surface-initiated Homogenous Nucleation Surface Nucleation Comment

We investigate theoretical, laboratory, and atmospheric evidence for a recently proposed hypothesis: homogenous ice nucleation occurs at the surface, not in the volume, of supercooled water drops. Using existing thermodynamic arguments, laboratory experiments , and atmospheric data, we conclude that ice embryo formation at the surface 5 cannot be confirmed or disregarded. Ice nucleation rates measured as a function of drop size in an air ambient could help distinguish between volume and surface nucle-ation rates.
Recognition of Modern Arabic Poems

We propose a machine learning method for recognizing modern Arabic poems based on the common poetic features of modern Arabic poetry. The poetic features include: rhyming, repetition, use of diacritics and punctuations, and text alignment. The method can classify text documents as poem or non-poem documents with a very high accuracy of 99.81%.
Risk factors influencing the outcome of peptic ulcer bleeding in chronic kidney disease after initial endoscopic hemostasis

AbstractPatients with chronic kidney disease (CKD) who had peptic ulcer bleeding (PUB) may have more adverse outcomes. This population-based cohort study aimed to identify risk factors that may influence the outcomes of patients with CKD and PUB after initial endoscopic hemostasis. Data from 1997 to 2008 were extracted from the National Health Insurance Research Database in Taiwan. We included a cohort dataset of 1 million randomly selected individuals and a dataset of patients with CKD who were alive in 2008. A total of 18,646 patients with PUB were screened, and 1229 patients admitted for PUB after endoscopic hemostasis were recruited. The subjects were divided into non-CKD (n = 1045) and CKD groups (n = 184). We analyzed the risks of peptic ulcer rebleeding, sepsis events, and mortality among in-hospital patients, and after discharge. Results showed that the rebleeding rates associated with repeat endoscopic therapy (11.96% vs 6.32%, P = 0.0062), death rates (8.7%, vs 2.3%, P < 0.0001), hospitalization cost (US$ 5595±7200 vs US$2408 ± 4703, P < 0.0001), and length of hospital stay (19.6 ± 18.3 vs 11.2 ± 13.1, P < 0.0001) in the CKD group were higher than those in the non-CKD group. The death rate in the CKD group was also higher than that in the non-CKD group after discharge. The independent risk factor for rebleeding during hospitalization was age (odds ratio [OR], 1.02; P = 0.0063), whereas risk factors for death were CKD (OR, 2.37; P = 0.0222), shock (OR, 2.99; P = 0.0098), and endotracheal intubation (OR, 5.31; P < 0.0001). The hazard ratio of rebleeding risk for aspirin users after discharge over a 10-year follow-up period was 0.68 (95% confidence interval [CI]: 0.45–0.95, P = 0.0223). On the other hand, old age (P < 0.0001), CKD (P = 0.0090), diabetes (P = 0.0470), and congestive heart failure (P = 0.0013) were the independent risk factors for death after discharge. In-hospital patients with CKD and PUB after endoscopic therapy had higher recurrent bleeding, infection, and mortality rates, and the need for second endoscopic therapy. Age was the independent risk factor for recurrent bleeding during hospitalization. After being discharged with a 10-year follow-up period, nonaspirin user was a significant factor for recurrent bleeding.
Optimum selection diversity for BPSK signals in Rayleigh fading channels

We propose a new selection diversity scheme that selects the branch providing the largest magnitude of the log-likelihood ratio (LLR). The LLR for BPSK signals in fading channels is found to be proportional to the product of the fading amplitude and the matched filter output. The proposed selection diversity scheme is shown to minimize the bit error rate (BER), and outperform existing selection diversity schemes. It is shown that the proposed scheme provides the same BER provided by the maximal ratio combining (MRC) scheme for a dual diversity system, and is only 0.3 dB inferior to the MRC when the number of branches is four, in Rayleigh fading channels.
User resistance factors in post ERP implementation

Enterprise resource planning (ERP) systems are becoming mature technologies to support inter- and intra-company business processes. However, one of the factors frequently cited as the major reason for the failure of ERP system in post implementation is “User Resistance”. ERP implementation doesn’t finish after Go-Live, instead the real test of system starts when user begins using the system. The main purpose of this study is to investigate user resistance factors in ERP post implementation stage and the influence between the factors associated with the research model, then to provide recommendations and guideline to avoid user resistance in ERP post implementation. To achieve this objectives quantitative method were conducted with 95 ERP end users. Correlation analysis is used to investigate the influence between user resistances as well as mean, std. deviation and rank. The result shows Resistance due to change, Change in Job content, User Expectations, Increased efforts, Lack of Education and User training, Usability issues and resistance to technology, Lack of user involvement in the development process, and Lack of communication between top management and end users are the factors behind user resistance. Recommendations and guideline to avoid user resistance in ERP post implementation are also presented. An equally important future direction is a psychological understanding of the users’ perspectives, Attitude strength, Attitude structure, and Resistance to change. For the user, there may be negative perceptions towards the ERP systems and the changes; however, the attitude strength and structure has not been examined. The benefits and outcomes of this study shall aid organizations to overcome user resistance in post ERP implementation.
Psychological controversies in gastroparesis: A systematic review

AIM To systematically review literature addressing three key psychologically-oriented controversies associated with gastroparesis. METHODS A comprehensive search of PubMed, CINAHL, and PsycINFO databases was performed to identify literature addressing the relationship between gastroparesis and psychological factors. Two researchers independently screened all references. Inclusion criteria were: an adult sample of gastroparesis patients, a quantitative methodology, and at least one of the following: (1) evaluation of the prevalence of psychopathology; (2) an outcome measure of anxiety, depression, or quality of life; and (3) evidence of a psychological intervention. Case studies, review articles, and publications in languages other than English were excluded from the current review. RESULTS Prevalence of psychopathology was evaluated by three studies (n = 378), which found that combined anxiety/depression was present in 24% of the gastroparesis cohort, severe anxiety in 12.4%, depression in 21.8%-23%, and somatization in 50%. Level of anxiety and depression was included as an outcome measure in six studies (n = 1408), and while limited research made it difficult to determine the level of anxiety and depression in the cohort, a clear positive relationship with gastroparesis symptom severity was evident. Quality of life was included as an outcome measure in 11 studies (n = 2076), with gastroparesis patients reporting lower quality of life than population norms, and a negative relationship between quality of life and symptom severity. One study assessed the use of a psychological intervention for gastroparesis patients (n = 120) and found that depression and gastric function were improved in patients who received psychological intervention, however the study had considerable methodological limitations. CONCLUSION Gastroparesis is associated with significant psychological distress and poor quality of life. Recommendations for future studies and the development of psychological interventions are provided.
Characterization of some antimicrobial substances from seed coat of Tamarindus indica Linn.

Tamarindus indica is a well known fruit used widely in India, as it forms a seasoning in many foods. However, its preservative nature is very short lived as both malate and tartarate can be easily metabolized by many microorganisms. In this study an attempt has been made to investigate the inhibitory effect of the seed coat extract prepared in methanol, ethanol and acetone which showed the presence of other substances like furfural and its derivatives, levuglucosan, tetrazene, cyclohexasiloxane, dioxalene, etc. The microorganisms used were Staphylococcus aureus, Salmonella typhimurium and Pseudomonas aeruginosa.