Miracle-dz/UniFAR-FTUs huggingface dataset:
Tree decompositions and social graphs

Abstract Recent work has established that large informatics graphs such as social and information networks have non-trivial tree-like structure when viewed at moderate size scales. Here, we present results from the first detailed empirical evaluation of the use of tree decomposition (TD) heuristics for structure identification and extraction in social graphs. Although TDs have historically been used in structural graph theory and scientific computing, we show that—even with existing TD heuristics developed for those very different areas—TD methods can identify interesting structure in a wide range of realistic informatics graphs. Our main contributions are the following: we show that TD methods can identify structures that correlate strongly with the core-periphery structure of realistic networks, even when using simple greedy heuristics; we show that the peripheral bags of these TDs correlate well with low-conductance communities (when they exist) found using local spectral computations; and we show that several types of large-scale “ground-truth” communities, defined by demographic metadata on the nodes of the network, are well-localized in the large-scale and/or peripheral structures of the TDs. Our other main contributions are the following: we provide detailed empirical results for TD heuristics on toy and synthetic networks to establish a baseline to understand better the behavior of the heuristics on more complex real-world networks; and we prove a theorem providing formal justification for the intuition that the only two impediments to low-distortion hyperbolic embedding are high tree-width and long geodesic cycles. Our results suggest future directions for improved TD heuristics that are more appropriate for realistic social graphs.
Novel Mutations in a Patient Isolate of Streptococcus agalactiae with Reduced Penicillin Susceptibility Emerging after Long-Term Oral Suppressive Therapy

ABSTRACT Penicillin nonsusceptibility has been demonstrated in group B streptococci (GBS), but there is limited information regarding mechanisms of resistance. We report a case of GBS with reduced susceptibility to penicillin emerging after long-term suppressive oral penicillin therapy for a prosthetic joint infection. Molecular characterization of the isolate before and after long-term penicillin therapy revealed 5 mutations in the ligand-binding regions of PBP1a, -2a, and -2x not previously reported in GBS.
A Regularized Estimator For Linear Regression Model With Possibly Singular Covariance

A regularized estimator is proposed for regression models in the case where the covariances may be singular. Conditions guaranteeing proximity of a regularized estimator to the optimal estimator are obtained by appropriate choice of regularization parameters by allowing a prescribed level of uncertainty. A simple Monte-Carlo simulation study is reported to highlight some aspects and performance of the proposed approach.
A Journey to the Core of the Blogosphere

Blogs are popular communication instruments in today's web and altogether, they form the so-called blogosphere. This blogosphere has repeatedly been subject to structural analyses, and one of the findings has been the discovery of the A-List phenomenon, a cohesive group of influential blogs in the center of the blogosphere, whose exact identification remained an open issue. We use four language-specific subsets of the blogosphere, for which we aggregated the blogroll-based networks. We adapt core theory to analyse and compare the cohesion in these four data-sets, and provide a new scalable method for the identification of core-periphery structures in blog networks, which can contribute to identify A-List blogs more reliably.
X‐ray compatible radiofrequency coil for magnetic resonance imaging

The range of RF coils that can be used in combined X‐ray/MR (XMR) systems is limited because many conventional coils contain highly X‐ray attenuating materials that are visible in the X‐ray images and potentially obscure patient anatomy. In this study, an X‐ray compatible coil design that has minimal X‐ray attenuation in the field of view (FOV) of the X‐ray image is presented. In this design, aluminum is used for the loop conductor and discrete elements of the coil are eliminated from the X‐ray FOV. A surface coil and an abdominal phased array coil were built using the X‐ray compatible design. X‐ray attenuation and MR imaging properties of the coils were evaluated and compared to conventional coils. The X‐ray compatible phased array coil was used to image patients during two interventional procedures in the XMR system. The X‐ray compatible coils allowed for fluoroscopic X‐ray image acquisition, without degradation by the coil, while maintaining excellent MR imaging qualities. Magn Reson Med 53:1409–1414, 2005. © 2005 Wiley‐Liss, Inc.
The Making of Meaning

This article presents a general theory of text processing that delineates the parallel operations in reading and writing. In particular, the theory discusses (1) common information location and retrieval procedures, (2) shared cognitive strategies employed to transform background knowledge into a text world, and (3) the role of context in the production of meaning.
TNF‐α induced over‐expression of GFAP is associated with MAPKs

Increased levels of tumor necrosis factor-alpha (TNF-α), a pluripotent cytokine that is reportedly mitogenic to astrocytes, are associated with the expression of glial fibrillary acidic protein (GFAP), the most specific marker for astrocytes, in many neuropathological conditions, including brain injury, CNS infection, Creutzfeldt-Jakob disease and Alzheimer's disease. Here, we show that treatment of cultured astrocytes with TNF-α resulted in dramatic over-expression of GFAP, associated with a substantial activation of the mitogen activated protein kinase (MAPK) Erk2 (extracellular signal-regulated protein kinase). We also demonstrate that TNF-α-induced over-expression of GFAP was significantly attenuated by the MAPK inhibitor PD98059. We conclude that TNF-α may up-regulate GFAP through the MAPK signaling pathway. Because increased GFAP is a hallmark of reactive gliosis, understanding the mechanisms that regulate GFAP expression may facilitate development of strategies to minimize the gliosis associated with many brain diseases.
Gut hormones in the treatment of short-bowel syndrome and intestinal failure

Purpose of reviewThe approval of teduglutide, a recombinant analog of human glucagon-like peptide (GLP) 2, by the US Food and Drug Administration (Gattex) and the European Medicines Agency (Revestive) has illustrated the potential of selected gut hormones as treatments in patients with short-bowel syndrome and intestinal failure. Gut hormones may improve the structural and functional intestinal adaptation following intestinal resection by decreasing a rapid gastric emptying and hypersecretion, by increasing the intestinal blood flow, and by promoting intestinal growth. This review summarizes the findings from phase 2 and 3 teduglutide studies, and pilot studies employing GLP-1 and agonists for this orphan condition. Recent findingsIn a 3-week, phase 2, metabolic balance study, teduglutide increased the intestinal wet weight absorption by approximately 700 g/day and reduced fecal energy losses by approximately 0.8 MJ/day (∼200 Kcal/day). In two subsequent 24-week, phase 3 studies, teduglutide reduced the need for parenteral support in the same magnitude. Adverse events were mainly of gastrointestinal origin and consistent with the known mechanism of action of teduglutide. Pilot studies suggest that GLP-1 may be less potent. Synergistic effects may be seen by co-treatment with GLP-2. SummaryGut hormones promote intestinal adaptation and absorption, decreasing fecal losses, thereby decreasing or even eliminating the need for parenteral support. This will aid the intestinal rehabilitation in these severely disabled short-bowel syndrome patients.
On the Local Structure of Stable Clustering Instances

We study the classic k-median and k-means clustering objectives in the beyond-worst-case scenario. We consider three well-studied notions of structured data that aim at characterizing real-world inputs:&#x2022; Distribution Stability (introduced by Awasthi, Blum, and Sheffet, FOCS 2010)&#x2022; Spectral Separability (introduced by Kumar and Kannan, FOCS 2010)&#x2022; Perturbation Resilience (introduced by Bilu and Linial, ICS 2010)We prove structural results showing that inputs satisfying at least one of the conditions are inherently local. Namely, for any such input, any local optimum is close both in term of structure and in term of objective value to the global optima.As a corollary we obtain that the widely-used Local Search algorithm has strong performance guarantees for both the tasks of recovering the underlying optimal clustering and obtaining a clustering of small cost. This is a significant step toward understanding the success of local search heuristics in clustering applications.
The Quest for a General and Reliable Fungal DNA Barcode

DNA sequences are key elements for both identification and classification of living organisms. Mainly for historical reasons, a limited number of genes are currently used for this purpose. From a mathematical point of view, any DNA segment, at any location, even outside of coding regions and even if they do not align, could be used as long as PCR primers could be designed to amplify them. This paper describes two methods to search genomic data for the most efficient DNA segments that can be used for identification and classification.
Delayed mTOR Inhibition with Low Dose of Everolimus Reduces TGFβ Expression, Attenuates Proteinuria and Renal Damage in the Renal Mass Reduction Model

Background The immunosuppressive mammalian target of rapamycin (mTOR) inhibitors are widely used in solid organ transplantation, but their effect on kidney disease progression is controversial. mTOR has emerged as one of the main pathways regulating cell growth, proliferation, differentiation, migration, and survival. The aim of this study was to analyze the effects of delayed inhibition of mTOR pathway with low dose of everolimus on progression of renal disease and TGFβ expression in the 5/6 nephrectomy model in Wistar rats. Methods This study evaluated the effects of everolimus (0.3 mg/k/day) introduced 15 days after surgical procedure on renal function, proteinuria, renal histology and mechanisms of fibrosis and proliferation. Results Everolimus treated group (EveG) showed significantly less proteinuria and albuminuria, less glomerular and tubulointerstitial damage and fibrosis, fibroblast activation cell proliferation, when compared with control group (CG), even though the EveG remained with high blood pressure. Treatment with everolimus also diminished glomerular hypertrophy. Everolimus effectively inhibited the increase of mTOR developed in 5/6 nephrectomy animals, without changes in AKT mRNA or protein abundance, but with an increase in the pAKT/AKT ratio. Associated with this inhibition, everolimus blunted the increased expression of TGFβ observed in the remnant kidney model. Conclusion Delayed mTOR inhibition with low dose of everolimus significantly prevented progressive renal damage and protected the remnant kidney. mTOR and TGFβ mRNA reduction can partially explain this anti fibrotic effect. mTOR can be a new target to attenuate the progression of chronic kidney disease even in those nephropathies of non-immunologic origin.
The Narrow Notion of Realism in Human Geography

The paper provides an analysis of the reception of realism in human geography. Gaps are identified between geographers' realism and realism as conceived by philosophers of science. The paper first outlines philosophers' abstract or thin 'CoreRealism' in simple ontological, semantic, and epistemological terms. It then shows how human geographers' 'GeoRealism' has concretised and thickened this core notion by incorporating a specific metaphysics of causation, a specific metaphysics of society, and a specific methodological doctrine about how to conduct (empirical) research. Additionally, GeoRealism has neglected central concerns of contemporary philosophy of science: the ontology of existence, the semantics of truth, and the epistemology of warranted belief. This has resulted in a notion of realism that is narrow in terms of its domain of application and its philosophical resources. The domain narrowness of GeoRealism may lead to inaccurate attitudes and antipluralist policies towards theories and approaches that are compatible with the broader CoreRealism. The resource narrowness of GeoRealism threatens to weaken its capacities to reflect critically on social constructivist and other allegedly antirealist trends as well as on the radical fallibility of human geographic theories and explanations. The paper offers an account of GeoRealism as an outgrowth of historically contingent circumstances and suggests that human geographers would benefit from reconsidering their understanding of realism within the broader perspective of philosophical literature.
Shoot and Root Traits Contribute to Drought Resistance in Recombinant Inbred Lines of MD 23–24 × SEA 5 of Common Bean

Drought is the major abiotic stress factor limiting yield of common bean (Phaseolus vulgaris L.) in smallholder systems in Latin America and eastern and southern Africa; where it is a main source of protein in the daily diet. Identification of shoot and root traits associated with drought resistance contributes to improving the process of designing bean genotypes adapted to drought. Field and greenhouse studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia to determine the relationship between grain yield and different shoot and root traits using a recombinant inbred lines (RILs) population (MD23–24 × SEA 5) of common bean. The main objectives of this study were to identify: (i) specific shoot and root morpho-physiological traits that contribute to improved resistance to drought and that could be useful as selection criteria in breeding beans for drought resistance; and (ii) superior genotypes with desirable shoot and root traits that could serve as parents in breeding programs that are aimed at improving drought resistance. A set of 121 bean genotypes (111 RILs, 2 parents, 8 checks) belonging to the Mesoamerican gene pool and one cowpea variety were evaluated under field conditions with two levels of water supply (irrigated and rainfed) over three seasons. To complement field studies, a greenhouse study was conducted using plastic cylinders with soil inserted into PVC pipes, to determine the relationship between grain yield obtained under field conditions with different root traits measured under greenhouse conditions. Resistance to drought stress was positively associated with a deeper and vigorous root system, better shoot growth, and superior mobilization of photosynthates to pod and seed production. The drought resistant lines differed in their root characteristics, some of them with a vigorous and deeper root system while others with a moderate to shallow root system. Among the shoot traits measured, pod harvest index, and seed number per area could serve as useful selection criteria for assessing sink strength and for genetic improvement of drought resistance in common bean.
Developmental coordination disorder: Current issues.

The concept of a specific disorder of motor function has been recognized for at least a century, with a gradual increase in awareness of this condition among health professionals and researchers developing over the past 30 years or so. First recognized in DSM-III-R (American Psychiatric Association 1987) as clumsy child syndrome, a number of labels have been applied to the disorder, including dyspraxia (Denckla 1984) and Specific Developmental Disorder of Motor Function (World Health Organization 1992). At present, however, common international approval has been expressed in favour of the term Developmental Coordination This idiopathic disorder is diagnosed in children who, for no medical reason , fail to acquire adequate motor skills. Typically, motor milestones are generally achieved rather late, while core aspects of this disorder can include difficulties in manual dexterity, ball skills and/or balance. Such marked impairment has a significant , negative impact on activities of daily living, such as dressing, eating, riding a bicycle, and/or on academic achievements, primarily as a result of poor handwriting skills (Barnett & Henderson 2005). DCD is not a trivial disorder as it affects around 5% of school-aged children, with a prevalence of boys over girls (3:1). Its onset is apparent in the early years, but usually it is not diagnosed formally before the age of 5 years. It has a varying, but significant, impact throughout the lifespan, and its symptoms are consistent across culture, race, socioeconomic status and gender. Although the long-term prognosis of individuals with DCD is uncertain, adolescence and adulthood is characterized by persistent motor difficulties, in addition to social problems as well as medical and psychiatric consequences (Cousins & Smyth 2005). In the past 30 years, diagnosis of this condition, development of assessment tools and research into the disorder has evolved. While much remains to be done to increase awareness, further strides are being made. This is particularly apparent when considering the level of attendance at international conferences on DCD, the latest of which triggered the papers published in this special issue. The Sixth International Conference on Developmental Coordination Disorder (DCD-VI), organized by Drs Stefania Zoia and Aldo Scabar (Institute of Child Health, IRCCS Burlo Garofolo, Trieste) and held in Trieste, Italy, saw 180 delegates from around the world attend a 4-day conference. The programme was very full and stimulating, with studies on research methods, postural control, sensorimo-tor control, handwriting, co-occurrence with other developmental disorders and intervention being presented …
A minimal-incision technique in total hip arthroplasty does not improve early postoperative outcomes. A prospective, randomized, controlled trial.

BACKGROUND Minimally invasive total hip arthroplasty has stirred substantial controversy with regard to whether it provides superior outcomes compared with total hip arthroplasty performed through longer incisions. The orthopaedic literature is deficient in well-designed scientific studies to support the clinical superiority of this approach. The objective of this study was to compare the results of a single mini-incision approach with those of a standard-incision total hip arthroplasty in the early postoperative period. METHODS Two hundred and nineteen patients (219 hips) admitted for unilateral total hip arthroplasty between December 2003 and June 2004 were randomized to undergo surgery through a short incision of <or=10 cm or a standard incision of 16 cm. All patients were blinded to the size of the incision for the duration of the hospital stay. The anesthetic, analgesic, and postoperative physiotherapy protocols were standardized, with the staff also blinded to the technique used. A single surgeon, who had performed more than 300 short-incision hip replacements prior to the start of this study and who performs an average of 415 primary total hip replacements a year, performed all procedures through a single-incision posterior approach using a cementless cup and cemented stem. RESULTS The two groups were matched for age, grade according to the system of the American Society of Anesthesiologists, and body mass index. No significant difference was detected with respect to postoperative hematocrit, blood transfusion requirements, pain scores, or analgesic use. We found no difference in early walking ability or length of hospital stay and no difference in component placement, cement-mantle quality, or functional outcome scores at six weeks. The patient variables significantly associated with a probability of early discharge independent of incision length were patient age and preoperative hemoglobin levels (p < 0.05). The surgical scars contracted significantly over six weeks (p < 0.05) but by a similar proportion of 11% to 12% in both groups. CONCLUSIONS Minimally invasive total hip arthroplasty performed through a single-incision posterior approach by a high-volume hip surgeon with extensive experience in less invasive approaches to the hip is safe and reproducible. However, it offers no significant benefit in the early postoperative period compared with a standard incision of 16 cm. As it is not known whether lower-volume and less-experienced surgeons can achieve similar results, the mini-incision technique merits further study before wide dissemination and implementation of this family of surgical approaches can be recommended.
Protein fold recognition with adaptive local hyperplane algorithm

Protein fold recognition task is important for understanding the biological functions of proteins. The adaptive local hyperplane (ALH) algorithm has been shown to perform better than many other renown classifiers including support vector machines, K-nearest neighbor, linear discriminant analysis, K-local hyperplane distance nearest neighbor algorithms and decision trees on a variety of data sets. In this paper, we apply the ALH algorithm to well-known data sets on protein fold recognition task without sequence similarity from Ding and Dubchak (2001). The results obtained demonstrate that the ALH algorithm outperforms all the seven other very well known and established benchmarking classifiers applied to same data sets.
[Ovulatory mucus and its pH, arborization and spermagglutination antibodies in women with fertility disorders].

OBJECTIVE We studied pH of ovulatory mucus, sperm penetration through capillary filled with ovulatory mucus in one hour and presence of local spermagglutinating antibodies. METHODS We measured pH, arborization and Kremer test in ovulatory mucus in 127 women with fertility disorder. Indirect mixed antiimunoglobulin reaction test (i-MAR-test for IgG, IgA, IgM and IgE) was used for detection of spermagglutinating antibodies. RESULTS pH 7.4-9.6 (physiological limit) was found in 94/127 women (74%), pH < 7.4 in 33 women (26%). 60% of 94 patients with physiological pH had Kremer's test above 2cm/hour (normal sperm penetration in ovulatory mucus), in 40% of them reduction of sperm penetration (< 2cm/hour, swelling, shaking, cytotoxicity) was seen. Sperm antibodies in ovulatory mucus in 24% patients with pH < 7.4 and 22% patients with physiological pH were studied. In 111 patients with regular menstrual cycle a classical arborization was found in 81%, in 14% was not proved. In 16 patients with irregular menstrual cycle classical arborization was observed in 11 of them. Local sperm antibodies were detected only in 13% of the total count of patients, it means in 17 patients. Their ovulatory mucus showed classical arborization. 30 healthy fertile women created the control group, only one secretion had pathological findings in all studied parameters owing to latent mycotic infection. SUMMARY Pathological pH of ovulatory mucus, hormonal dysbalance, and presence of local spermagglutinating antibodies evidently influence penetration of sperm cells through cervix uteri. Otherwise pathological microbial vaginal environment can start a cross reaction with the surface microbes and sperm epitopes. One sign of ovulation, arborization of cervical ovulatory mucus, is not connected directly with the presence of local sperm antibodies, but insufficient estrogen influence is a sign of the reduced immunosuppression in cervix area.