Miracle-dz/UniFAR-FTUs huggingface dataset:
The relationship between the electrochemical proton gradient and active transport in Escherichia coli membrane vesicles.

In the previous paper [ramos, S. , and Kaback, H.R. (1977), Biochemistry 16 (preceding paper in this issue)], it was demonstrated that Escherichia coli membrane vesicles generate a large electrochemical proton gradient (delta-muH+) under appropriate conditions, and some of the properties of delta-muH+ and its component forces [i.e., the membrane potential (delta psi) and the chemical gradient of protons (deltapH)] were described. In this paper, the relationship between delta-muH+, delta psi, and deltapH and the active transport of specific solutes is examined. Addition of lactose or glucose 6-phosphate to membrane vesicles containing the appropriate transport systems results in partial collapse of deltapH, providing direct evidence for the suggestion that respiratory energy can drive active transport via the pH gradient across the membrane. Titration studies with valinomycin and nigericin lead to the conclusion that, at pH 5.5, there are two general classes of transport systems: those that are driven primarily by delta-muH+ (lactose, proline, serine, glycine, tyrosine, glutamate, leucine, lysine, cysteine, and succinate) and those that are driven primarily by deltapH (glucose 6-phosphate, D-lactate, glucuronate, and gluconate). Importantly, however, it is also demonstrated that at pH 7.5, all of these transport systems are driven by delta psi which comprises the only component of delta-muH+ at this external pH. In addition, the effect of external pH on the steady-state levels of accumulation of different solutes is examined, and it is shown that none of the pH profiles correspond to those observed for delta-muH+, delta psi, or deltapH. Moreover, at external pH values above 6.0-6.5, delta-muH+ is insufficient to account for the concentration gradients established for each substrate unless the stoichiometry between protons and accumulated solutes is greater than unity. The results confirm many facets of the chemiosmotic hypothesis, but they also extend the concept in certain important respects and allow explanations for some earlier observations which seemed to preclude the involvement of chemiosmotic phenomena in active transport.
Emotion Recognition through Physiological Signals for Human-Machine Communication

The ability to recognize emotion is one of the hallmarks of emotion intelligence. This paper proposed to recognize emotion using physiological signals obtained from multiple subjects. IAPS (International Affective Picture System) images were used to elicit target emotions. Five physiological signals: Blood volume pulse (BVP), Electromyography (EMG), Skin Conductance (SC), Skin Temperature (SKT) and Respiration (RESP) were selected to extract 30 features for recognition. Two pattern classification methods, Fisher discriminant and SVM method are used and compared for emotional state classification. The experimental results indicate that the proposed method provides very stable and successful emotional classification performance as 92% over six emotional states.
Design of Experiments-Based Monitoring of Critical Quality Attributes for the Spray-Drying Process of Insulin by NIR Spectroscopy

Moisture content and aerodynamic particle size are critical quality attributes for spray-dried protein formulations. In this study, spray-dried insulin powders intended for pulmonary delivery were produced applying design of experiments methodology. Near infrared spectroscopy (NIR) in combination with preprocessing and multivariate analysis in the form of partial least squares projections to latent structures (PLS) were used to correlate the spectral data with moisture content and aerodynamic particle size measured by a time of flight principle. PLS models predicting the moisture content were based on the chemical information of the water molecules in the NIR spectrum. Models yielded prediction errors (RMSEP) between 0.39% and 0.48% with thermal gravimetric analysis used as reference method. The PLS models predicting the aerodynamic particle size were based on baseline offset in the NIR spectra and yielded prediction errors between 0.27 and 0.48 μm. The morphology of the spray-dried particles had a significant impact on the predictive ability of the models. Good predictive models could be obtained for spherical particles with a calibration error (RMSECV) of 0.22 μm, whereas wrinkled particles resulted in much less robust models with a Q2 of 0.69. Based on the results in this study, NIR is a suitable tool for process analysis of the spray-drying process and for control of moisture content and particle size, in particular for smooth and spherical particles.
Severe Acute Respiratory Syndrome Coronavirus Gene 7 Products Contribute to Virus-Induced Apoptosis

ABSTRACT The proteins encoded by gene 7 of the severe acute respiratory syndrome coronavirus (SARS-CoV) have been demonstrated to have proapoptotic activity when expressed from cDNA but appear to be dispensable for virus replication. Recombinant SARS-CoVs bearing deletions in gene 7 were used to assess the contribution of gene 7 to virus replication and apoptosis in several transformed cell lines, as well as to replication and pathogenesis in golden Syrian hamsters. Deletion of gene 7 had no effect on SARS-CoV replication in transformed cell lines, nor did it alter the induction of early apoptosis markers such as annexin V binding and activation of caspase 3. However, viruses with gene 7 disruptions were not as efficient as wild-type virus in inducing DNA fragmentation, as judged by terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) staining, indicating that the gene 7 products do contribute to virus-induced apoptosis. Disruption of gene 7 did not affect virus replication or morbidity in golden Syrian hamsters, suggesting that the gene 7 products are not required for acute infection in vivo. The data indicate that open reading frames 7a and 7b contribute to but are not solely responsible for the apoptosis seen in SARS-CoV-infected cells.
Improving the Accuracy and Speed of Support Vector Machines

Support Vector Learning Machines (SVM) are finding application in pattern recognition, regression estimation, and operator inversion for ill-posed problems. Against this very general backdrop, any methods for improving the generalization performance, or for improving the speed in test phase, of SVMs are of increasing interest. In this paper we combine two such techniques on a pattern recognition problem. The method for improving generalization performance (the "virtual support vector" method) does so by incorporating known invariances of the problem. This method achieves a drop in the error rate on 10,000 NIST test digit images of 1.4% to 1.0%. The method for improving the speed (the "reduced set" method) does so by approximating the support vector decision surface. We apply this method to achieve a factor of fifty speedup in test phase over the virtual support vector machine. The combined approach yields a machine which is both 22 times faster than the original machine, and which has better generalization performance, achieving 1.1 % error. The virtual support vector method is applicable to any SVM problem with known invariances. The reduced set method is applicable to any support vector machine.
TRAViz: A Visualization for Variant Graphs

This article describes the development and application of an innovative tool, Text Re-use Alignment Visualization (TRAViz), whose aim is to visualize variation between editions of both historical and modern texts. Reading different editions of a text empowers research in literary studies and linguistics, where one can study a text’s reception or follow the development of its language over time. One of the purposes of a text edition is to trace or reconstruct a possible archetype or something that might be considered to be an original version of the text in order to better understand its evolution over time. To do so, the textual scholar examines and records the similarities and the differences between a number of exemplars in what is known as a ‘critical apparatus’. The result of this variant analysis can be visually represented as a ‘Variant Graph’, where the relationships between these exemplars can be more easily studied. Variant Graphs can be, in turn, visualized in order to facilitate reading and interaction with the source data. Borrowing from existing digital tools, TRAViz assists the scholar in the collation process by specifically focusing on design and user engagement, concurrently seeking to simplify interaction as a means of encouraging humanists to adopt the tool. The article will describe the needs and rationale behind the creation of TRAViz by exploring existing research, describing its functionality through examples, and by finally discussing how its application can influence future development of this tool in particular and of the field in general.
Top-k subgraph matching query in a large graph

Recently, due to its wide applications, subgraph search has attracted a lot of attention from database and data mining community. Sub-graph search is defined as follows: given a query graph Q, we report all data graphs containing Q in the database. However, there is little work about sub-graph search in a single large graph, which has been used in many applications, such as biological network and social network. In this paper, we address top-k sub-graph matching query problem, which is defined as follows: given a query graph Q, we locate top-k matchings of Q in a large data graph G according to a score function. The score function is defined as the sum of the pairwise similarity between a vertex in Q and its matching vertex in G. Specifically, we first design a balanced tree (that is G-Tree) to index the large data graph. Then, based on G-Tree, we propose an efficient query algorithm (that is Ranked Matching algorithm). Our extensive experiment results show that, due to efficiency of pruning strategy, given a query with up to 20 vertices, we can locate the top-100 matchings in less than 10 seconds in a large data graph with 100K vertices. Furthermore, our approach outperforms the alternative method by orders of magnitude.
ASR, dialects, and acoustic/phonological distances

If the acoustic models in an ASR system have been built using standard pronunciations in the acoustic training database, dialect speakers usually show in a test a lower ASR performance compared to speakers of standard pronunciations. In this paper, this degree of degradation is considered to be a measure for the distance between dialect and standard pronunciation. We relate this ASR-distance with a phonologically based distance between dialect and standard pronunciation. It is concluded that phonological and acoustically based distance measures are in line with each other, but this conclusion is tentative due to the degrees of uncertainty in all measurements. Simple lexical modifications based on phonological knowledge to accommodate with the dialectal pronunciations were only moderately successful.
Finnish norms for young children on the Strengths and Difficulties Questionnaire

Abstract Background: Early recognition of children's mental health problems is crucial. Although the Strengths and Difficulties Questionnaire (SDQ) is a commonly used screening method, further research is needed on its validity and norms for young children. Aims: The aims of the study were to confirm the adjusted lower (normal/borderline) and upper (borderline/abnormal) cut-offs for the SDQ in a Finnish community sample of 4–9-year-old children, and to explore the SDQ's ability to identify the children with mental health problems. Methods: Parents and teachers completed the SDQs (n = 2666). The Development and Well-Being Assessment (DAWBA) was administered to parents and teachers of 646 children. Results: The overall participation rate was 57%. The suggested cut-offs for the SDQ total difficulties scale rated by parents and teachers were 2–5 points lower than the corresponding published British norms. The sensitivity for the total score normal/borderline cut-off (9/10) was 76% in the parent and 66% in the teacher reports and for the borderline/abnormal cut-off (11/12) 90% and 70% respectively. The respective specificity values were 69%, 63%, 74% and 66%. The area under curve (AUC) values of the higher cut-offs were good for parent (0.87) and satisfactory for teacher rated (0.76) total scores. The presence of a DAWBA-rater assigned diagnosis in the abnormal group compared with the normal group was sixfold in the parent and threefold in the teacher reported SDQs. Conclusions: The suggested cut-offs were clearly lower than the British norms. Yet the properties of the method's discriminative validity were acceptable. Population specific norms, taking into account both the culture and children's age, seem necessary for screening and for international comparisons of the method's validity properties.
Progesterone Receptor Isoform-Specific Promoter Methylation: Association of PRA Promoter Methylation with Worse Outcome in Breast Cancer Patients

Purpose: ERα and PR levels are critical determinants for breast cancer prognosis and response to endocrine therapy. Although PR is known to be silenced by methylation of its promoter, few studies have correlated methylation with PR levels and outcome in breast cancer. There is only one previous small study comparing methylation of the two PR isoforms, PRA and PRB, which are expressed from different promoters, and finally, there is no prior knowledge of associations between isoform-specific methylation and outcome. Experimental Design: We conducted a cohort-based study to test for associations between PRA and PRB methylation, expression, and clinical outcome in tamoxifen-treated patients (n = 500), and in patients who underwent surgery only (n = 500). Methylation and PR levels were measured by bisulfite pyrosequencing and ligand-binding assay, respectively. Results: Low PR levels were significantly associated with worse outcome in all patients. PRA and PRB promoters were methylated in 9.6% and 14.1% of the breast tumors, respectively. The majority (74%) of PR-negative tumors were not methylated despite the significant inverse correlation of methylation and PR levels. PRA methylation was significantly associated with PRB methylation, although a subset of tumors had PRA only (3.9%) or PRB only (8.3%) methylated. Methylation of PRA, but not PRB was significantly associated with worse outcome in the tamoxifen-treated group. Conclusions: Mechanisms other than promoter methylation may be more dominant for loss of PR. Isoform-specific methylation events suggest independent regulation of PRA and PRB. Finally, this article shows for the first time that PRA methylation plays a unique role in tamoxifen-resistant breast cancer. Clin Cancer Res; 17(12); 4177–86. ©2011 AACR.
Novel targeted therapies in chordoma: an update

Chordomas are rare, locally aggressive skull base neoplasms known for local recurrence and not-infrequent treatment failure. Current evidence supports the role of maximal safe surgical resection. In addition to open skull-base approaches, the endoscopic endonasal approach to clival chordomas has been reported with favorable albeit early results. Adjuvant radiation is prescribed following complete resection, alternatively for gross residual disease or at the time of recurrence. The modalities of adjuvant radiation therapy reported vary widely and include proton-beam, carbon-ion, fractionated photon radiotherapy, and photon and gamma-knife radiosurgery. As of now, no direct comparison is available, and high-level evidence demonstrating superiority of one modality over another is lacking. While systemic therapies have yet to form part of any first-line therapy for chordomas, a number of targeted agents have been evaluated to date that inhibit specific molecules and their respective pathways known to be implicated in chordomas. These include EGFR (erlotinib, gefitinib, lapatinib), PDGFR (imatinib), mTOR (rapamycin), and VEGF (bevacizumab). This article provides an update of the current multimodality treatment of cranial base chordomas, with an emphasis on how current understanding of molecular pathogenesis provides a framework for the development of novel targeted approaches.
Exposure to diesel exhaust upregulates COX-2 expression in ApoE knockout mice

Introduction: We have shown that diesel exhaust (DE) inhalation caused progression of atherosclerosis; however, the mechanisms are not fully understood. We hypothesize that exposure to DE upregulates cyclooxygenase (COX) expression and activity, which could play a role in DE-induced atherosclerosis. Methods: ApoE knockout mice (30-week old) fed with regular chow were exposed to DE (at 200 µg/m3 of particulate matter) or filtered air (control) for 7 weeks (6 h/day, 5 days/week). The protein and mRNA expression of COX-1 and COX-2 were evaluated by immunohistochemistry analysis and quantitative real-time PCR, respectively. To examine COX activity, thoracic aortae were mounted in a wire myograph, and phenylephrine (PE)-stimulated vasoconstriction was measured with and without the presence of COX antagonists (indomethacin). COX-2 activity was further assessed by urine 2,3-dinor-6-keto PGF1α level, a major metabolite of prostacyclin I2 (PGI2). Results: Immunohistochemistry analysis demonstrates that DE exposure enhanced COX-2 expression in both thoracic aorta (p < 0.01) and aortic root (p < 0.03), with no modification of COX-1 expression. The increased COX-2 expression was positively correlated with smooth muscle cell content in aortic lesions (R2 = 0.4081, p < 0.008). The fractional changes of maximal vasoconstriction in the presence of indomethacin was attenuated by 3-fold after DE exposure (p < 0.02). Urine 2,3-dinor-6-keto PGF1α level was 15-fold higher in DE group than the control (p < 0.007). The mRNA expression of COX-2 (p < 0.006) and PGI synthase (p < 0.02), but not COX-1, was significantly augmented after DE exposure. Conclusion: We show that DE inhalation enhanced COX-2 expression, which is also associated with phenotypic changes of aortic lesion.
Impact of Human Mobility on the Design of Opportunistic Forwarding Algorithms

Studying transfer opportunities between wireless devices carried by humans, we observe that the distribution of the inter-contact time, that is the time gap separating two contacts of the same pair of devices, exhibits a heavy tail such as one of a power law, over a large range of value. This observation is confirmed on six distinct experimental data sets. It is at odds with the exponential decay implied by most mobility models. In this paper, we study how this new characteristic of human mobility impacts a class of previously proposed forwarding algorithms. We use a simplified model based on the renewal theory to study how the parameters of the distribution impact the delay performance of these algorithms. We make recommendation for the design of well founded opportunistic forwarding algorithms, in the context of human carried devices.
Management of Myofascial Pain: Low-Level Laser Therapy Versus Occlusal Splints

The present study was designed to compare the effects of low-level laser with occlusal splints in patients with signs and symptoms of myofascial pain (MP) dysfunction syndrome. A total of 40 (34 women and 6 men, with a mean age of 32.84 [SD, 10.70] years) were selected after the diagnosis of MP according to the Research Diagnostic Criteria for Temporomandibular Disorder. The patients were randomly divided into 2 groups: study group (n = 20) and control group (n = 20). Low-level laser was applied to patients in the study group 2 times per week, for a total of 10 sessions. Patients in the control group were instructed to wear occlusal splints 24 h/d for 3 months. The functional examination was based on Research Diagnostic Criteria for Temporomandibular Disorder and pressure pain threshold values were obtained with the aid of an algometer in both groups. Patients' self-report of pain was evaluated with visual analog scale. Comparisons were made within and between the groups before and after treatment. Vertical movements showed statistically significant improvements after the treatments in both groups (P < 0.01), but when the groups were compared with each other, there were no significant difference between the groups. In both groups, tenderness to palpation of the muscles decreased significantly. Pressure pain threshold evaluations and visual analog scale scores revealed similar results, too. This particular type of low-level laser therapy (820 nm, 3 J/cm2, 300-mW output power) is as effective as occlusal splint in pain release and mandibular movement improvement in MP.
Effects of Changes in BI-RADS Density Assessment Guidelines (Fourth Versus Fifth Edition) on Breast Density Assessment: Intra- and Interreader Agreements and Density Distribution.

OBJECTIVE The objective of our study was to determine intra- and interreader agreements for density assessment using the fifth edition of the BI-RADS guidelines and to compare with those for density assessment using the fourth edition of the BI-RADS guidelines. MATERIALS AND METHODS Five radiologists assessed breast density four times in 104 mammographic examinations: twice using the fourth edition of the BI-RADS guidelines and twice using the fifth edition. The intra- and interreader agreements for density assessment based on each guideline were determined and compared. The density distribution pattern under each of the four BI-RADS density categories using each guideline was also noted and compared. RESULTS The intrareader agreement for density assessment using the fifth-edition criteria was lower than that using the fourth-edition criteria (p = 0.0179). The overall intrareader agreement (weighted kappa) using the old criteria was 0.84 (95% CI, 0.80-0.87), and the individual intrareader agreement values in five readers ranged from 0.78 (95% CI, 0.69-0.88) to 0.92 (95% CI, 0.87-0.97). The overall intrareader agreement using the new BI-RADS criteria was 0.77 (95% CI, 0.73-0.81), and the individual intrareader agreement values in five readers ranged from 0.74 (95% CI, 0.64-0.84) to 0.99 (95% CI, 0.98-1.00). The interreader agreement values obtained using the fifth-edition criteria were also lower than those obtained using the fourth-edition criteria (p = 0.006). The overall interreader agreement using the old BI-RADS criteria was 0.65 (95% CI, 0.61-0.69), whereas the overall interreader agreement using the new BI-RADS criteria was 0.57 (95% CI, 0.53-0.61). Overall a higher number of dense assessments were given when the fifth-edition guidelines were used (p < 0.0001). CONCLUSION Compared with the intra- and interreader agreements obtained using the fourth edition of the BI-RADS guidelines, the intra- and interreader agreements were lower using the fifth-edition guidelines. An increased number of dense assessments were given when the fifth-edition guidelines were used.
The Influence of Fairness Perceptions and Goal Commitment on Managers' Performance in a Budget Setting

Recent budgeting research suggests that fairness perceptions play a role in performance. In particular, prior work demonstrates a positive relation between fairness and performance during budgeting. The process by which fairness perceptions translate into improved performance, however, remains unaddressed. This study contributes to the accounting literature by investigating whether fairness perceptions improve performance via participation by increasing managers' commitment to budgetary goals. Structural equation models are proposed in which both fairness perceptions and goal commitment influence managers' performance during budgeting. Questionnaire data collected from one field site in the midst of downsizing were used to test the models. The results suggest that increased participation during budgeting fosters a sense of fairness, which, in turn, increases managers' commitment to budgetary goals and subsequently enhances performance ratings. The direct path between fairness perceptions and performance, .