Miracle-dz/UniFAR-FTUs huggingface dataset:
O2 Reactions at the Six-iron Active Site (H-cluster) in [FeFe]-Hydrogenase*

Irreversible inhibition by molecular oxygen (O2) complicates the use of [FeFe]-hydrogenases (HydA) for biotechnological hydrogen (H2) production. Modification by O2 of the active site six-iron complex denoted as the H-cluster ([4Fe4S]-2FeH) of HydA1 from the green alga Chlamydomonas reinhardtii was characterized by x-ray absorption spectroscopy at the iron K-edge. In a time-resolved approach, HydA1 protein samples were prepared after increasing O2 exposure periods at 0 °C. A kinetic analysis of changes in their x-ray absorption near edge structure and extended X-ray absorption fine structure spectra revealed three phases of O2 reactions. The first phase (τ1 ≤ 4 s) is characterized by the formation of an increased number of Fe–O,C bonds, elongation of the Fe–Fe distance in the binuclear unit (2FeH), and oxidation of one iron ion. The second phase (τ2 ≈ 15 s) causes a ∼50% decrease of the number of ∼2.7-Å Fe–Fe distances in the [4Fe4S] subcluster and the oxidation of one more iron ion. The final phase (τ3 ≤ 1000 s) leads to the disappearance of most Fe–Fe and Fe–S interactions and further iron oxidation. These results favor a reaction sequence, which involves 1) oxygenation at 2FeH+ leading to the formation of a reactive oxygen species-like superoxide (O2−), followed by 2) H-cluster inactivation and destabilization due to ROS attack on the [4Fe4S] cluster to convert it into an apparent [3Fe4S]+ unit, leading to 3) complete O2-induced degradation of the remainders of the H-cluster. This mechanism suggests that blocking of ROS diffusion paths and/or altering the redox potential of the [4Fe4S] cubane by genetic engineering may yield improved O2 tolerance in [FeFe]-hydrogenase.
Defective Generation of a Humoral Immune Response Is Associated with a Reduced Incidence and Severity of Collagen-Induced Arthritis in Microsomal Prostaglandin E Synthase-1 Null Mice1

Microsomal PGE synthase-1 (mPGES-1) is an inducible enzyme that acts downstream of cyclooxygenase and specifically catalyzes the conversion of PGH2 to PGE2. The present study demonstrates the effect of genetic deletion of mPGES-1 on the developing immunologic responses and its impact on the clinical model of bovine collagen-induced arthritis. mPGES-1 null and heterozygous mice exhibited decreased incidence and severity of arthritis compared with wild-type mice in a gene dose-dependent manner. Histopathological examination revealed significant reduction in lining hyperplasia and tissue destruction in mPGES-1 null mice compared with their wild-type littermates. mPGES-1 deficient mice also exhibited attenuation of mechanical nociception in a gene dose-dependent manner. In addition, mPGES-1 null and heterozygous mice showed a marked reduction of serum IgG against type II collagen, including subclasses IgG1, IgG2a, IgG2b, IgG2c, and IgG3, compared with wild-type mice, which correlated with the reduction in observed inflammatory features. These results demonstrate for the first time that deficiency of mPGES-1 inhibits the development of collagen-induced arthritis, at least in part, by blocking the development of a humoral immune response against type II collagen. Pharmacologic inhibition of mPGES-1 may therefore impact both the inflammation and the autoimmunity associated with human diseases such as rheumatoid arthritis.
Within-patient variability of (18)F-FDG: standardized uptake values in normal tissues.

UNLABELLED The aim of this study was to evaluate the test-retest variability of standardized uptake values (SUVs) in normal tissues and the impact of various methods for measuring the SUV. METHODS SUVs were determined in 70 cancer-free patients (40 female and 30 male) on 2 occasions an average of 271 d apart. Mean values for body weight and height, blood glucose level, injected dose, and uptake period did not change between the 2 groups of studies. Four regions of interest (ROIs) were placed-on the liver, lung, mediastinum, and trapezius muscle. Mean and maximum SUVs normalized for body weight were obtained, and normalizations were then applied for lean body mass (LBM), LBM and blood glucose level, body surface area (BSA), and BSA and blood glucose level. RESULTS In the lungs and muscle, metabolic activity within the ROIs was significantly different in the 2 studies, no matter which method was used for the SUVs. The differences ranged from 0.02 to 0.1 for SUV normalized for body weight and SUV normalized for LBM and from 0.001 to 0.002 for SUV normalized for BSA. In the liver, results were similar for all SUVs, except for maximum SUV corrected for LBM and maximum SUV corrected for LBM and blood glucose level. The metabolic activity measured in the mediastinum was also comparable in the 2 studies, regardless of the type of SUV. When investigating whether any normalization method for SUVs reduces variability and improves test-retest concordance, we found no significant superiority for any. The best intraclass correlation coefficients were obtained with the SUV normalized for body weight, in both the liver and the mediastinum, but the coefficients of variation were similar for all 3 mean SUVs that were not corrected for glucose level (range, 10.8%-13.4%). However, normalizing for blood glucose level increased the variability and decreased the level of concordance between studies. CONCLUSION The SUVs measured in normal liver and mediastinum in cancer-free patients are stable over time, no matter which normalization is used. Correcting for blood glucose level increases the variability of the values and should therefore be avoided. Normalizing for BSA or LBM does not improve the reproducibility of the measurements.
Phase III trial of bevacizumab (BEV) in the primary treatment of advanced epithelial ovarian cancer (EOC), primary peritoneal cancer (PPC), or fallopian tube cancer (FTC): A Gynecologic Oncology Group study.

LBA1 Background: BEV, a humanized anti-VEGF monoclonal antibody, has demonstrated single-agent activity in patients with recurrent EOC, or PPC. The therapeutic impact of concurrent ± maintenance BEV with standard chemotherapy (CT) was evaluated in an international, double-blind, placebo-controlled phase III trial. METHODS Eligible patients had newly diagnosed, previously untreated EOC, PPC or FTC following abdominal surgery for staging and maximal effort at tumor debulking; stage III (macroscopic residual disease) or stage IV disease. The randomly allocated regimens were (1) CT (IV paclitaxel 175 mg/m2 + carboplatin AUC 6 cycles 1-6) + placebo cycles (C)2-22 (R1) (2) CT + concurrent BEV (15 mg/kg) C2-6 + placebo C7-22 (R2) (3) CT + concurrent BEV C2-6 + maintenance BEV C7-22 (R3) Infusions were administered d1 of a 21d cycle. The primary endpoint is progression-free survival (PFS) (radiographic, CA125, clinical criteria or death); secondary endpoints include overall survival, safety, and QoL. RESULTS 1,873 patients, median age 60, were enrolled from 9/05 - 6/09. Stage III optimally debulked (34%), stage III sub-optimally debulked (40%), and stage IV (26%) patients were similarly distributed in each treatment group. Grade 3 - 4 hypertension was reported in 1.6% (R1), 5.4% (R2), and 10.0% (R3). Grade ≥ 3 GI perforation, hemorrhage or fistula occurred in 0.8% (R1), 2.6% (R2) and 2.3% (R3). Relative to R1, the hazard of first progression or death for R2 was 0.908 (95% CI: 0.795 - 1.04, p=0.16) and for R3 was 0.717 (95% CI: 0.625 - 0.824, p<0.0001). CONCLUSIONS This study demonstrates that front-line treatment of EOC, PPC, and FTC patients with CT plus concurrent and maintenance BEV prolongs PFS. This is the first anti-angiogenic agent to demonstrate benefit in this population. [Table: see text].
Activities of enzymes that hydrolyze adenine nucleotides in lymphocytes from patients with rheumatoid arthritis

The purpose of this study was to investigate the activities of ecto‐nucleoside triphosphate diphosphohydrolase (E‐NTPDase; EC 3.6.1.5; CD39) and adenosine deaminase (E‐ADA; EC 3.5.4.4) in lymphocytes from patients with rheumatoid arthritis (RA). Thirty patients diagnosed with RA through American College of Rheumatology criteria as well as 30 healthy patients were selected. Peripheral blood lymphocytes were isolated, and E‐NTPDase and E‐ADA activities were assayed. The results demonstrated an increased E‐NTPDase activity (both ATP and ADP as substrates) and a decreased E‐ADA activity in RA patients. These data suggest an organic effort to preserve the adenosine level, which is known to have anti‐inflammatory and analgesic properties, working as a potent suppressor of immune response. Copyright © 2012 John Wiley & Sons, Ltd.
2D Particle-In-Cell simulation on rising-sun magnetron

Two original methods applied to 2D PIC code are set out. One of them concerns the emission of particle related to the potential difference imposed between electrodes. The other one deals with the modelling of the transition between resonant cavity and wave-guide by local lossy medium. Finally, results in good agreement with the experiment on the rising-sun magnetron AX9 are presented.
Type checking annotation-based product lines

Software product line engineering is an efficient means of generating a family of program variants for a domain from a single code base. However, because of the potentially high number of possible program variants, it is difficult to test them all and ensure properties like type safety for the entire product line. We present a product-line-aware type system that can type check an entire software product line without generating each variant in isolation. Specifically, we extend the Featherweight Java calculus with feature annotations for product-line development and prove formally that all program variants generated from a well typed product line are well typed. Furthermore, we present a solution to the problem of typing mutually exclusive features. We discuss how results from our formalization helped implement our own product-line tool CIDE for full Java and report of our experience with detecting type errors in four existing software product line implementations.
SALICYLIC ACID PREVENTS THE DAMAGING ACTION OF STRESS FACTORS ON WHEAT PLANTS

We investigated the effect of salicylic acid (SA) on plant resistance to environmental stress factors. Treatment of wheat plants with 0.05 mM SA increased the level of cell division within the apical meristem of seedling roots which caused an increase in plant growth. Phytohormones are known to play a key role in plant growth regulation. It was found that the SA treatment caused accumulation of both ABA and IAA in wheat seedlings. However, the SA treatment did not influence cytokinin content. We suppose, that the protective and growth promoting effects of SA are due to the phenomenon described above. The SA treatment reduced the damaging action of salinity and water deficit on seedling growth and accelerated a restoration of growth processes.Treatment with SA essentially diminished the alteration of phytohormones levels in wheat seedlings under salinity and water deficit. The SA treatment prevented the decrease in IAA and cytokinin content completely which reduced stress-induced inhibition of plant growth. Also, high ABA levels were maintained in SA treated wheat seedlings which provided the development of antistress reactions, for example, maintenance of proline accumulation. Thus protective SA action includes the development of antistress programs and acceleration of normalization of growth processes after removal stress factors.
Efficient implementation of the HMARM model identification and its application in spectral analysis

The Hidden Markov Auto-Regressive model (HMARM) has recently been proposed to model non-Gaussian AutoRegressive signals with hidden Markov-type driving noise. This model has been shown to be suitable to many signals, including voiced speech and digitally modulated signals received through ISI channels. The HMARM facilitates a blind system identification algorithm that has a good computational efficiency and data efficiency. In this paper, we solve an implementation issue of the HMARM identification, which can otherwise degrade the efficiency of the model and hinder extensive evaluations of the algorithm. Then we study in more detail the properties associated with the autoregressive (AR) spectral analysis for signals of interest.
Tobacco smoking in treatment-resistant schizophrenia patients is associated with impaired cognitive functioning, more severe negative symptoms, and poorer social adjustment

Tobacco smoking is common in schizophrenia patients. It has been reported that schizophrenia patients who are tobacco smokers have better cognitive performances compared to those who are nonsmokers. However, little is known on the effects of tobacco smoking in treatment-resistant schizophrenia (TRS) patients. The aim of this study was to compare cognitive performances, psychotic symptoms, and social adjustment in tobacco smoker TRS patients compared to nonsmoker TRS patients. Smoker and nonsmoker TRS patients did not differ in demographics and in mean daily antipsychotic dose. Smoker TRS patients had significantly higher scores than nonsmoker patients on the positive and negative syndrome scale (PANSS) and on the negative symptoms subscale. These patients also performed worse than nonsmoker patients on problem-solving cognitive domain. Social adjustment was not significantly different between the two groups. In both groups of patients, worse cognitive performances were mostly predicted by higher severity of negative symptoms. Worse performances on the verbal memory and problem-solving cognitive domains were correlated with social-functioning impairment in tobacco smoker TRS patients but not in nonsmoker ones. The results showed that tobacco smoking was not significantly associated with better cognitive performances in TRS patients, while it was significantly associated with higher negative symptoms. Even if a direct causative mechanism cannot be inferred and despite the fact that these patients may use tobacco to self-medicate, it could be speculated that these associations may, at least partially, be related to a tobacco-smoking–induced worsening of abnormal dopamine dysfunction, which has been suggested to occur in TRS patients.
Managerial Attitudes Toward Stakeholder Salience Within Selected Western Pacific-Rim Economies

ABSTRACT This study empirically examines the attitudes of managers and managerial students in Australia, China and Indonesia, toward the perceived prominence of selected organisational stakeholders. A development model is used to argue that Australian respondents will perceive greater equality in prominence between the selected organisational stakeholders than their Chinese and Indonesian counterparts. Results indicated that Chinese respondents attributed greater prominence toward Government as an organisational stakeholder, and contrary to expectations, perceived greater equality (less variance) in prominence between stakeholders. The study provides a basis on which further work on the perceptions of stakeholder prominence can be undertaken in different contexts.
Pattern of head and neck malignant tumours in a Nigerian teaching hospital--a ten year review.

BACKGROUND In Nigeria record of incidence and pattern of Head and Neck malignancies is scanty. In our Hospital, there had been no prior published report on this subject. OBJECTIVE To study the pattern of occurrence of Head and Neck malignancies treated in Obafemi Awolowo university Hospitals Complex, Ile Ife, Nigeria. METHODS medical records of patients with histopathologically confirmed head and neck malignancies over a 10 year period (1989--1998) were analyzed. MAIN RESULTS Three hundred and thirteen (313) cases, made up of 184 (59%) males and 129 (41%) females were found. The most common sites for head and neck malignancies were found to be in the oral cavity (36.8%), the neck (26.8 %), the thyroid (13.7 %), and the esophagus (5.1%). The paranasal sinuses and the ear were the least affected anatomical sites with one (0.3 %) of cases each. The histopathological tumour types found in this work were lymphoma (40.26%), squamous cell carcinoma (25.23%), sarcoma (2.6%), while many other minor histopathological variants accounted for 31.9%. Lymphoma was the most common in children, while carcinoma was found in, and forms the most common histopathological variant of head and neck malignancies in the older age group. PRINCIPAL CONCLUSIONS There is a high incidence of childhood head and neck malignancies found in this study in contrast to the Western literature where the highest incidence is found in the older age group and the elderly. Jaw malignancies constituted the most common malignancies of the oral cavity. Lymphoma and thyroid malignancies are relatively common in our center.
Differential effects of tar content, type of tobacco and use of a filter on lung cancer risk in male cigarette smokers.

BACKGROUND To date, the effect of tar exposure, the use of a filter and the type of tobacco (light or dark) on the risk of lung cancer have not been studied together. METHODS Data from a case-control study on lung cancer were used to evaluate the specific effects of these three parameters. Cases of lung cancer and controls were interviewed in hospitals in France from 1976 to 1980. The past tar content of cigarettes distributed by the French Tobacco Monopoly was obtained. The results presented concern an exclusively male population of lifelong smokers of French cigarettes and lifelong smokers of light imported cigarettes. The population comprised 1114 cases of histologically confirmed lung cancer and 1466 hospitalized controls. RESULTS An increase in risk was found among smokers of both dark and light cigarettes (relative risk [RR] = 2.6, 95% confidence interval [CI]:1.1-6.5) and among lifelong smokers of dark cigarettes (RR = 1.7, 95% Cl: 0.9-3.2) compared to lifelong smokers of light cigarettes. Similarly, the risk of lung cancer was higher among smokers of both non-filter and filter cigarettes (RR = 1.6, 95% Cl: 0.9-2.7) and among lifelong smokers of non-filter cigarettes (RR = 1.6, 95% Cl: 0.9-2.8) than among lifelong smokers of filter cigarettes. A borderline significant increase in risk was observed for smokers of French cigarettes compared to smokers of light imported cigarettes (RR = 2.6, 95% Cl: 0.9-7.7). No significant difference in the risk of lung cancer was observed among smokers of French cigarettes according to the proportion of years of smoking high tar cigarettes. CONCLUSION This study tends to demonstrate a separate effect of type of tobacco, use of a filter and tar content in addition to the usual characteristics of cigarette smoking on lung cancer risk.
Sketch-based Shape Retrieval using Pyramid-of-Parts

We present a multi-scale approach to sketch-based shape retrieval. It is based on a novel multi-scale shape descriptor called Pyramidof- Parts, which encodes the features and spatial relationship of the semantic parts of query sketches. The same descriptor can also be used to represent 2D projected views of 3D shapes, allowing effective matching of query sketches with 3D shapes across multiple scales. Experimental results show that the proposed method outperforms the state-of-the-art method, whether the sketch segmentation information is obtained manually or automatically by considering each stroke as a semantic part.
Factors influencing the outcome of lower‐extremity diabetic ulcers treated with hyperbaric oxygen therapy

The objectives of this study were to report outcomes of a large number of patients receiving hyperbaric oxygen therapy (HBO2T) for diabetic lower‐extremity ulcers, and to identify likely outcome predictors. Five hyperbaric facilities supplied data on 1,006 patients. A sixth clinic served as a validation sample for the regression‐based prediction model, and later additional data from Memorial Hermann Hospital were added. The severity of lower‐extremity lesions was assessed upon initiation of HBO2T using the Modified Wagner scale, and the outcome described as healed, partially healed, not improved, amputated, or died. Overall, 73.8% of patients improved (granulated or healed). Factors significantly related to outcome included renal failure, pack‐year smoking history, transcutaneous oximetry, number of HBO2T treatments, and interruption of treatment regimen. Number of treatments per week and treatment pressure (2.0 vs. 2.4 atmospheres absolute) were not significant factors in outcome. Concomitant administration of autologous growth factor gel did not improve outcome. A multiple regression model was fitted to the data that can be used to predict the outcome of diabetic patients undergoing HBO2T. Given the high cost of amputation and rehabilitation, these data suggest that hyperbaric oxygen treatment should be an important adjunctive therapy to heal lower‐extremity lesions, especially those with a Wagner grade of 3 or higher.
Processing of Fear and Anger Facial Expressions: The Role of Spatial Frequency

Spatial frequency (SF) components encode a portion of the affective value expressed in face images. The aim of this study was to estimate the relative weight of specific frequency spectrum bandwidth on the discrimination of anger and fear facial expressions. The general paradigm was a classification of the expression of faces morphed at varying proportions between anger and fear images in which SF adaptation and SF subtraction are expected to shift classification of facial emotion. A series of three experiments was conducted. In Experiment 1 subjects classified morphed face images that were unfiltered or filtered to remove either low (<8 cycles/face), middle (12–28 cycles/face), or high (>32 cycles/face) SF components. In Experiment 2 subjects were adapted to unfiltered or filtered prototypical (non-morphed) fear face images and subsequently classified morphed face images. In Experiment 3 subjects were adapted to unfiltered or filtered prototypical fear face images with the phase component randomized before classifying morphed face images. Removing mid frequency components from the target images shifted classification toward fear. The same shift was observed under adaptation condition to unfiltered and low- and middle-range filtered fear images. However, when the phase spectrum of the same adaptation stimuli was randomized, no adaptation effect was observed. These results suggest that medium SF components support the perception of fear more than anger at both low and high level of processing. They also suggest that the effect at high-level processing stage is related more to high-level featural and/or configural information than to the low-level frequency spectrum.
Analyzing the Energy-Latency Trade-Off During the Deployment of Sensor Networks

The inherent trade-off between energy-efficiency and rapidity of event dissemination is characteristic for wireless sensor networks. Scarcity of energy renders it necessary for nodes to spend a large portion of their lifetime in an energyefficient sleep mode during which they do neither receive nor send messages. On the other hand, the longer nodes stay in sleep mode, the slower will be the reaction time for disseminating an external event. The trade-off is prominently exhibited during the deployment phase of sensor networks, if some nodes are deployed earlier than others. In this paper, we study this fundamental trade-off by giving a formal model that enables us to compare the performance of different protocols and algorithms. Based on this model, we propose, analyze, and simulate two novel algorithms which significantly outperform existing solutions.