Miracle-dz/UniFAR-FTUs huggingface dataset:
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets

Here we present version 2.0 of HADDOCK, which incorporates considerable improvements and new features. HADDOCK is now able to model not only protein–protein complexes but also other kinds of biomolecular complexes and multi‐component (N > 2) systems. In the absence of any experimental and/or predicted information to drive the docking, HADDOCK now offers two additional ab initio docking modes based on either random patch definition or center‐of‐mass restraints. The docking protocol has been considerably improved, supporting among other solvated docking, automatic definition of semi‐flexible regions, and inclusion of a desolvation energy term in the scoring scheme. The performance of HADDOCK2.0 is evaluated on the targets of rounds 4‐11, run in a semi‐automated mode using the original information we used in our CAPRI submissions. This enables a direct assessment of the progress made since the previous versions. Although HADDOCK performed very well in CAPRI (65% and 71% success rates, overall and for unbound targets only, respectively), a substantial improvement was achieved with HADDOCK2.0. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A major step towards individualized therapy of lung cancer with gefitinib: the IPASS trial and beyond

Most patients with non-small-cell lung cancer (NSCLC) present with advanced disease and have poor long-term prognosis. Gefitinib, a targeted therapy that prevents ATP binding in the tyrosine kinase domain of the EGF receptor, has been subject to comprehensive clinical development. A Phase III trial has demonstrated that gefitinib is superior to carboplatin/paclitaxel in terms of progression-free survival and objective response rate, as first-line treatment for pulmonary adenocarcinoma among never-smokers or former light smokers in East Asia (the IRESSA™ Pan-Asia Study), with the presence of an EGFR mutation being a strong predictor of the effect of gefitinib compared with carboplatin/paclitaxel. In this article, these results are discussed in the context of other recently reported studies of EGFR mutation-positive patients in both Asian and non-Asian countries. Furthermore, the clinical implications and future challenges for gefitinib are highlighted.
Production of Tyzzer's disease in rats by ingestion of bacterial spores.

Tyzzer's disease was produced in rats by peroral inoculation with spores of Bacillus piliformis (Tyzzer's organism) of rat origin. After ingestion of 10(6) spores necrotized lesions with intracellular bacterial propagation were seen in the intestines, liver and heart on days 2 to 14 postinoculation (p.i.). A number of B. piliformis were present within enterocytes of the cecum and colon. Infected cells were also seen in the liver, myocardium and intestinal muscle layers on days 3 to 7 p.i. Infective spores were found to be shed in feces during 3 to 10 days p.i.
CCR4 and CAF1 deadenylases have an intrinsic activity to remove the post-poly(A) sequence

MicroRNAs (miRNAs) recruit the CCR4–NOT complex, which contains two deadenylases, CCR4 and CAF1, to promote shortening of the poly(A) tail. Although both CCR4 and CAF1 generally have a strong preference for poly(A) RNA substrates, it has been reported from yeast to humans that they can also remove non-A residues in vitro to various degrees. However, it remains unknown how CCR4 and CAF1 remove non-A sequences. Herein we show that Drosophila miRNAs can promote the removal of 3′-terminal non-A residues in an exonucleolytic manner, but only if an upstream poly(A) sequence exists. This non-A removing reaction is directly catalyzed by both CCR4 and CAF1 and depends on the balance between the length of the internal poly(A) sequence and that of the downstream non-A sequence. These results suggest that the CCR4–NOT complex has an intrinsic activity to remove the 3′-terminal non-A modifications downstream from the poly(A) tail.
Generation of a reference network for Ireland and its contribution to the design of an optical network architecture

Realistic reference networks are critical for all techno-economic evaluations in the design of an optical network architecture. As this information was not publicly available for Ireland, we generated such a reference network. In this paper we elaborate on the challenges faced during the generation and present some statistics. We also show how this is used in the design of an optical architecture for the same country. The level of detail of the reference network needed varies according to the layer of the architecture that is being designed. In this paper we show how the original reference network is reduced while maintaining important properties for the design of the architecture. We also elicit geotypes from the structure of the reference network and discus the importance of this computation in the design of the optical distribution network.
In Search of the Perfect Comorbidity Measure for Use With Administrative Claims Data: Does It Exist?

Background:Numerous measures of comorbidity have been developed for health services research with administrative claims. Objective:We sought to compare the performance of 4 claims-based comorbidity measures. Research Design and Subjects:We undertook a retrospective cohort study of 5777 Medicare beneficiaries ages 66 and older with stage III colon cancer reported to the Surveillance, Epidemiology, and End Results Program between January 1, 1992 and December 31, 1996. Measures:Comorbidity measures included Elixhauser’s set of 30 condition indicators, Klabunde’s outpatient and inpatient indices weighted for colorectal cancer patients, Diagnostic Cost Groups, and the Adjusted Clinical Group (ACG) System. Outcomes included receipt of adjuvant chemotherapy and 2 year noncancer mortality. Results:For all measures, greater comorbidity significantly predicted lower receipt of chemotherapy and higher noncancer death. Nested logistic regression modeling suggests that using more claims sources to measure comorbidity generally improves the prediction of chemotherapy receipt and noncancer death, but depends on the measure type and outcome studied. All 4 comorbidity measures significantly improved the fit of baseline regression models for both chemotherapy receipt (baseline c-statistic 0.776; ranging from 0.779 after adding ACGs and Klabunde to 0.789 after Elixhauser) and noncancer death (baseline c-statistic 0.687; ranging from 0.717 after adding ACGs to 0.744 after Elixhauser). Conclusions:Although some comorbidity measures demonstrate minor advantages over others, each is fairly robust in predicting both chemotherapy receipt and noncancer death. Investigators should choose among these measures based on their availability, comfort with the methodology, and outcomes of interest.
Cutaneous carbon dioxide monitoring in adults

Purpose of review Arterial blood gas analysis is the ‘gold standard’ method to measure the arterial partial pressure of carbon dioxide (PaCO2). However, arterial sampling including arterial catheterization is invasive and expensive. Cutaneous carbon dioxide tension (PcCO2) measurement is used as a noninvasive surrogate measure of PaCO2, which is used to either estimate PaCO2 or determine trend changes in the measurement. There has been considerable progress in the technical aspects of PcCO2 monitoring in the last few years. In this article, we evaluate recent developments and the renewed interest in the subject of PcCO2 monitoring in adults and discuss the technical aspects, clinical applications and the future outlook for this technique in the clinical setting. Recent findings With evolution in technology, PcCO2 monitoring is now less cumbersome than before. Combined PcCO2 measurement and pulse oximetry is now possible with a single earlobe sensor. Summary The clinical settings in which PcCO2 monitoring can be applied include patient monitoring during and after anaesthesia, patients receiving noninvasive ventilation, post extubation, endoscopy under sedation, the sleep laboratory and the lung function laboratory. Although there is an overlap of the clinical indications when both PcCO2 and end-tidal carbon dioxide monitoring may be used, it is our opinion that both these methods have independent indications and are sometimes also complementary to each other in patient care.
Mapping of genes and transcribed sequences in a gene rich 400-kb region on human chromosome 11p15.1→p14

We have identified a number of transcribed sequences within a 400-kb interval on chromosome 11p15.1→ p14. Six genes and 13 novel transcripts including ESTs, cDNAs and exons have been identified and assigned to this region. Comparison of mRNA sequence with genomic sequence has enabled us to determine the exon/intron structure of four of the genes (NUCB2, PIK3C2A, RPS13 and OR7E14P).
Diffusion tensor imaging in presymptomatic and early Huntington's disease: Selective white matter pathology and its relationship to clinical measures

Atrophy of cortical and subcortical gray matter is apparent in Huntington's disease (HD) before symptoms manifest. We hypothesized that the white matter (WM) connecting cortical and subcortical regions must also be affected early and that select clinical symptoms were related to systems degeneration. We used diffusion tensor magnetic resonance imaging (DTI) to examine the regional nature of WM abnormalities in early HD, including the preclinical period, and to determine whether regional changes correlated with clinical features. We studied individuals in early stages (HD), presymptomatic individuals known to carry the genetic mutation that causes HD (Pre‐HD), and matched healthy controls. DTI indices of tissue integrity were obtained from several regions of interest, including the corpus callosum (CC), internal capsule (IC), and basal ganglia, were compared across groups by t tests, and were correlated to cognitive and clinical measures. WM alterations were found throughout the CC, in the anterior and posterior limbs of the IC, and in frontal subcortical WM in HD subjects, supporting the selective involvement of the pyramidal tracts in HD; a similar distribution of changes was seen in Pre‐HD subjects, supporting presymptomatic alterations. There was a significant relationship between select DTI measures and cognitive performance. Alterations in diffusion indices were also seen in the striatum that were independent of atrophy. Our findings support that WM alterations occur very early in HD. The distribution of the changes suggests that these changes contribute to the disruption of pyramidal and extrapyramidal circuits and also support a role of compromised cortical circuitry in early cognitive and subtle motor impairment during the preclinical stages of HD. © 2006 Movement Disorder Society
Effect of feeding on olive oil and thyme on pregnancy and lactation periods

This study aimed to evaluate the effect of feeding on virgin olive oil (VOO) and extra virgin olive oil (EVOO) at 50% and 100% with or without thyme leaves at 1% and 2.5% on pregnancy and lactation periods. Methods: One hundred and twenty adult female rats (120 ±5g) were randomly divided into 15 groups (n=8) for month before mating. On 19th day of pregnancy, half of pregnant rats were weighted, killed and their fetuses take off with uterus. Another half of pregnant rats were left to evaluate the lactation period. Biochemical assays, bone measurements and fertility hormones were evaluated. Results: Generally, the VOO groups were improved the health status of pregnant and lactating rats more than EVOO groups. The pregnant rats in VOO and thyme leaves powder groups were lower of body weight gain (BWG) without their fetuses than EVOO and thyme leaves powder groups. The mean weight of fetuses in VOO and thyme leaves powder groups were higher than EVOO combined with thyme leaves groups. Also, the feeding on olive oils with thyme leaves had an increase of number of fetuses and bone Ca and P contents. The results showed that, in an increasing of number of fetuses caused decrease in bone mineral density (BMD). Pregnant and lactating rats fed on 100% olive oils had TC, TG, LDL-C, and VLDL-C lower than the rats fed on 50% olive oils. Also, the rats fed on olive oils and thyme leaves powder had increase in both E2 and progesterone levels before mating and at the end of lactation period compared to control group. Meanwhile, the prolactin hormone levels for rats at the end of lactation period were lower than on 19th day of pregnancy period. Conclusion: Diet which containing with olive oil improved the health status, especially during pregnancy and lactation periods. Consumption of olive oil and olive oil and thyme leaves could be reduce the risk of infertility in females.
Source coding with side information and a converse for degraded broadcast channels

Let \{(X_i, Y_i,)\}_{i=1}^{\infty} be a memoryless correlated source with finite alphabets, and let us imagine that one person, encoder 1, observes only X^n = X_1,\cdots,X_n and another person, encoder 2, observes only Y^n = Y_1,\cdots,Y_n . The encoders can produce encoding functions f_n(X^n) and g_n(Y^n) respectively, which are made available to the decoder. We determine the rate region in case the decoder is interested only in knowing Y^n = Y_1,\cdots,Y_n (with small error probability). In Section H of the paper we give a characterization of the capacity region for degraded broadcast channels (DBC's), which was conjectured by Bergmans [11] and is somewhat sharper than the one obtained by Gallager [12].
Medication adherence among psychotic patients before admission to inpatient treatment.

OBJECTIVE Nonadherence to antipsychotic regimens is considered to be one of the main reasons for hospital readmission. This study assessed the extent of nonadherence in the month before inpatient treatment. METHODS Ninety-five consecutive patients with an ICD-10 diagnosis of a psychotic disorder (F20) were surveyed about adherence at admission to psychiatric inpatient treatment at a hospital in Linz, Austria. Adherence was assessed on the basis of self-report and by interviewing multiple informants. Episodes of inpatient treatment during the year after discharge were assessed prospectively. RESULTS Fifty-four patients (57 percent) were rated as partially or fully nonadherent. Compared with patients with good adherence, those who were nonadherent had lower mean scores on the Global Assessment of Functioning (41.4 compared with 47.2), more often received compulsory treatment (52 percent compared with 22 percent), more often had impaired insight into their illness at admission (63 percent compared with 24 percent) and discharge (41 percent compared with 13 percent), and had more days of inpatient treatment in the year after discharge from the index episode (mean of 44.8 days compared with 20.6 days). Adherence was significantly better among patients in regular contact with their psychiatrist and among younger patients. Nonadherent patients who gained insight during treatment had significantly fewer days of inpatient treatment during the next year than those whose insight was still low at discharge (mean of 19.2 days compared with 73.2 days). CONCLUSIONS Nonadherence is an important contributor to the need for inpatient treatment and is associated with a less favorable course of treatment. The best predictor of further inpatient treatment is insight into illness at discharge.
Three Novel Mutations in SQSTM1 Identified in Familial Paget's Disease of Bone

Mutations in Sequestosome 1 (SQSTM1) have been shown to segregate with familial Paget's disease of bone (PDB). We examined the coding sequence of SQSTM1 in five PDB pedigrees and found three novel mutations clustered around the C‐terminal ubiquitin associated domain. Disruptions of the C‐terminal domain of SQSTM1 seem to be a leading cause of familial PDB.
“Only Two Months Destroys Everything”: A Case Study of Communication About Nonadherence to Antiretroviral Therapy in a South African HIV Pharmacy Context

Adherence to antiretroviral treatment (ART) is a complex phenomenon and patients do not always adhere for a variety of reasons. The quality of communication and the therapeutic relationship between health professionals and patients have an important influence on adherence, as do contextual and environmental factors. Little qualitative research exists that examines health care interactions in the context of adherence counselling. This article presents a case study of a discussion about nonadherence between a pharmacy assistant and a patient in a South African HIV context. A hybrid analytical approach revealed various themes such as how the topic of nonadherence is addressed, participants' responses to the patient's nonadherence, and the process of negotiating a new commitment to adherence. The case provides insight into the impact of contextual factors on the interaction and challenges involved in discussing nonadherence—in particular, the patient's attempts to save face, the pharmacy assistant's irritation and anger, and the patient's expressed regrets. This case raises questions around issues of patient agency. Health professionals are encouraged to consider the influence of context, lifeworld, and culture on patients' ability to adhere to treatment regimens. By working to improve communication processes and strengthen the therapeutic relationship, patients may be empowered to achieve better adherence levels.
Online platform supporting teaching correlation

A web platform (http://www.animation.statgrafia.pl/corr elation) accompanying a previous paper (Teach Stat31 (2009), 52-54) is described. The platform contains animations of a small simulation study based on the population presented in the above-mentioned paper, results of a similar but large simulation study based on the same population, and results of similar simulation studies based on seven 1000-element populations with various population correlation coefficients. With th e platform, a teacher can explain how sample size influences bias and prec ision of the regular estimator of Pearson's correlation coe fficient, and what in general the distribution of the correlation coefficient looks like.
Myocardial Glucose Uptake Evaluated by Positron Emission Tomography and Fluorodeoxyglucose During Hyperglycemic Clamp in IDDM Patients: Role of Free Fatty Acid and Insulin Levels

Myocardial and whole-body glucose metabolism was assessed in 19 insulin-dependent diabetes mellitus (IDDM) patients. A hyperglycemic clamp was performed 1) in the absence of insulin at free fatty acid (FFA) levels of 1.0 mmol/l (test 1); 2) in the absence of insulin at low FFA levels (0.1 mmol/l) by means of a lipid-lowering drug, acipimox (test 2); 3) during insulin infusion to achieve systemic levels of 400 pmol/l and FFA levels of 0.1 mmol/l (test 3); and 4) at the insulin levels of test 3 but increasing FFA to 1.0 mmol/l by means of heparin and intralipid infusion (test 4). Myocardial glucose uptake was measured by positron emission tomography (PET) and 2-[18F]fluoro-2-deoxy-D-glucose. Whole-body glucose uptake was measured in the four conditions by the glucose infusion rate during the PET scanning period. Myocardial glucose uptakes were 40.3 ± 18.0, 395.5 ± 139.6, 852.2 ± 99.1, and 1,388.4 ± 199.1 μmol · kg tissue−1 · min−1 (mean ± SD) and whole-body glucose uptakes were 10.1 ± 2.3, 10.1 ± 3.4, 42.8 ± 5.8, and 30.5 ± 5.6 μmol · kg body wt−1 · min−1 during tests 1, 2, 3, and 4, respectively. Thus, in IDDM patients without coronary artery disease under the condition of hyperglycemia, an increase of myocardial glucose uptake was obtained either by lowering of FFA levels during hypoinsulinemia or by an increase in FFA levels during hyperinsulinemia. In both conditions no significant changes of whole-body glucose uptake were demonstrated.
Linear Control and Parallel Distributed Fuzzy Control Design for T-S Fuzzy Time-Delay System

This paper studies the stabilization problem for T-S fuzzy systems with time delay. Based on Lyapunov criterion and Razumikhin theorem, two types of stabilizing controller are designed. One is the linear state feedback controller and the other is the parallel distributed fuzzy controller (PDFC). For each type of the controller, there are some derived sufficient conditions under which the whole closed loop fuzzy time-delay system is asymptotically stable. Moreover, those sufficient conditions can be transformed into the linear matrix inequality (LMI) problem. Then the controllers can be obtained by solving LMIs. Finally, a practical continuous stirred tank reactor (CSTR) system illustrates the control design and its stabilization effectiveness.
LEPTIN AND ADIPONECTIN IN PANCREATIC CANCER smoking status , alcohol consumption , history of diabetes , and family history of pancreatic cancer

The aim of this study was to analyze the relationship of serum leptin as well as adiponectin and the manifestation of pancreatic cancer (PC). Serum leptin, adiponectin, glucose homeostasis and insulin resistance (expressed as HOMA-IR) were investigated in 64 patients with newly diagnosed PC and compared with 64 healthy controls (CON group) and 75 patients with type 2 diabetes (DM2). Seventy percent of newly diagnosed PC patients had DM2. The levels of leptin were lower, whilst adiponectin/leptin ratio was higher in PC patients (both with and without DM2), in comparison with CON and DM2 groups (P < 0.001) independently of age, BMI and waist circumference. Newly diagnosed PC is characterized with lower leptin concentrations and higher adiponectin/leptin ratio in comparison with CON or DM2 individuals. Analysis of these parameters could help in the screening of persons in high risk for PC, especially in those with DM2.
Almost-universal quadratic forms: An effective solution of a problem of Ramanujan

The object of this paper is to prove several results giving an effective method for deciding whether a positive definite integral quaternary quadratic form is almost universal, that is, whether it represents all large positive integers. In this way we obtain an effective and definitive solution to a problem first addressed and investigated by Ramanujan 90 years ago (cf. [11]). The following set Σ = {1, 2, 3, 5, 6, 7, 10, 14}
Algorithms and data structures for graph analysis

Introduction Software implementations for graph structures can represent a graph as an adjacency list or a sparse adjacency matrix. There are no standards regarding the implementation details of adjacency list or adjacency matrix structures. Notable parties propose different implementations for adjacency lists [1]. Guido van Rossum suggests using a hash table with arrays, where the arrays indicate edges to vertices. Cormen et al. [2] suggest using an array of singly linked lists. Goodrich and Tamassia propose dedicated objects for both vertices and edges, allowing for easily adding information to both vertices and edges. Each of the implementation suggestions has advantages and disadvantages. One can easily come up with more variations, but their trade-offs in the context of graph applications are not clear.