Miracle-dz/UniFAR-FTUs huggingface dataset:
Decomposition Techniques for Learning Graphical Models

Probabilistic graphical models are ubiquitous tools for reasoning under uncertainty that have been useful to many fields. Despite their importance, learning these models from incomplete data remains a challenge, due to the high non-convexity of the corresponding optimization problem. Iterative algorithms, such as Expectation Maximization (EM), are typically used for learning from incomplete data, yet these approaches tend to exhibit behaviors that are independent of the degree of incompleteness in the data. We argue in this thesis that the degree of incompleteness is a main indicator of the difficulty of a learning problem. As such, we investigate a number of learning approaches, which are driven and motivated by this degree. In particular, we show that by exploiting certain patterns in the dataset, the learning problem can be decomposed into smaller and independent learning problems, which can lead to orders-of-magnitude speed-up in learning time. Moreover, we propose a new class of algorithms for learning graphical models, whose learned parameters and running time improve as the data becomes less incomplete.
Inhibition of Spirochaeta aurantia chemotaxis by neurotoxins

The effects of neurotoxic compounds on the chemotactic response of Spirochaeta aurantia were investigated. In the presence of neurotoxins that affect action potential generation and transmission in excitable eucaryotic cells, D-xylose taxis was inhibited by 69 to 93%. Inhibition of chemotaxis was not due to decreased viability or motility. This study supports the hypothesis that the molecular basis for sensory signal transduction in S. aurantia involves ion fluxes across the cytoplasmic membrane.
Erythropoiesis Stimulatory Agent- Resistant Anemia in Dialysis Patients: Review of Causes and Management

Despite new therapeutic options and treatment strategies, anemia still remains one of the major complications of chronic kidney disease (CKD), especially in patients undergoing chronic hemodialysis for end-stage renal disease. Successful management of anemia is a central part of patient care that may improve clinical outcomes. Although the National Kidney Foundation Dialysis Outcomes Quality Initiative (NKF-DOQI) working group reformulated its recommendations by stating that the hemoglobin target in patients receiving erythropoiesis stimulatory agents (ESA) should generally be 11–12 g/dl, this target value can not be achieved in many of them, despite treatment with high doses of ESA. The aim of the present review is to provide an update of the recent literature on causes and possible management of ESA-resistant anemia in CKD patients.
Suggestive genetic linkage to chromosome 11p11.2‐q12.2 in hereditary prostate cancer families with primary kidney cancer

The Seattle‐based PROGRESS study was started in 1995 to ascertain hereditary prostate cancer (HPC) families for studies of genetic susceptibility. Subsequent studies by several research groups, including our own, suggest that HPC is a genetically heterogeneous disease. To be successful in mapping loci for such a complex disease, one must consider ways of grouping families into subsets that likely share the same genetic origin. Towards that end, we analyzed a genome‐wide scan of HPC families with primary kidney cancer.
3D microwave breast imaging based on multistatic radar concept system

Microwave imaging (MI) is one of the most promising and attractive new techniques for earlier breast-cancer detection. The microwave tomography (MT) realizes configuration of multistatic multiilumination system and reconstructs dielectric properties of the breast by solving a nonlinear inversion scattering problem. We describe below ETRI 3D MT system and 3D MI reconstruction program. Here we demonstrate also examples of image reconstruction using our MT system.
Letter: management of post‐operative Crohn's disease ‐ thiopurines vs adalimumab– authors' reply

SIRS, We thank Aguas et al. for their comments on our recent paper. 2 The POCER study demonstrated that following intestinal resection for Crohn’s disease clinical risk stratification and endoscopic monitoring of disease, with treatment intensification for early recurrence, was superior to optimised drug therapy without endoscopic monitoring. The only direct comparison of anti-tumour necrosis factor (TNF) vs. thiopurines in high-risk patients was undertaken at 6 months postoperatively; these data, together with those of Aguas et al., suggest that a top-down approach should be reserved for those at very high risk of post-operative recurrence. The POCER study aimed to decrease recurrent Crohn’s disease after resection. We acknowledge that perianal disease, extensive intestinal resection, and in particular myenteric and submucosal plexitis at the proximal margin of the resection are also considered to be risk factors for earlier post-operative recurrence However, the clinical factors (smoking, previous surgery, and penetrating disease) used in the POCER study to stratify patients have, in cohort studies, reflected the highest increased risk of recurrence. They are easily identifiable pre-operatively in clinical practice. The POCER study confirmed, for the first time prospectively, that these factors are predictors of recurrence, even in the setting of risk-stratified drug therapy. The Rutgeerts’ scoring system for post-operative recurrence, including the i2 score, has been shown previously to predict subsequent symptomatic recurrence. This scoring system has also been used in other randomised, controlled trials of drug therapy in the postoperative setting, with good discrimination between treatment arms. 9 In the POCER study, central reading and three other secondary measures of endoscopic disease activity were included: the Crohn’s Disease Endoscopic Index of Severity (CDEIS), the Simple Endoscopic Score for Crohn’s Disease (SES-CD) and a count of the number of ulcers at the anastomosis. The outcomes observed using these other endoscopic scoring systems, although they are not specific for the post-operative setting, provided strong support for the primary Rutgeerts’ measure used in this study. We believe that for the moment the Rutgeerts’ score offers the best scoring method. The APPRECIA and PREVENT studies are comparative drug studies, unlike the real-life POCER study that examined the optimal strategy for post-operative care, including the value of risk stratification, endoscopic intervention and treatment intensification for early recurrence. We believe there are sufficient comparative drug studies to appreciate the relative efficacy of available drugs. In contrast, we believe more strategic studies are needed in the field of inflammatory bowel disease.
Common Gene Polymorphisms in the Mother of a Child Born with Neural Tube Defect and Down Syndrome

The purpose of this communication is to report an unusual case of an infant affected with both neural tube defect (NTD) and Down syndrome (DS). Genetic risk factors in the mother were investigated. As impaired folate metabolism is implicated in the etiology of NTD and DS, folate gene polymorphisms were determined in the case-mother. These included methylene tetrahydrofolate reductase gene (MTHFR) 677C>T, methionine synthase gene (MTR) 2756A>G, betaine homocysteine methyl transferase gene (BHMT) 742G>A, thymidylate synthase gene enhancer region (TSER) – 3 or 2 tandem repeats of 28-bp and TS gene, 6-bp deletion in 3’ untranslated region. The genotype distribution and minor allele frequencies were also determined in a group of female control subjects. The genotypes of case-mother was MTHFR 677CT, MTR 2756AG, TSER 3R2R, TS D0D6 and BHMT 742AA. The BHMT 742AA genotype, in combination of genotypes of case-mother at five, four or three polymorphic loci, was either absent or present in a small number of control women. The case mother was a life-long vegetarian. Although the precise maternal risk factor(s) cannot be pin-pointed, it is possible that BHMT 742AA genotype coupled with restricted intake of those folate micronutrients present chiefly in foods of animal origin may play a role.
[2009] An Instruction Decomposition Method for Reconfigurable Decoders

Embedded multimedia processors are required to execute many kinds of traditional instruction sets. Since decomposition and translation of instructions by software emulators have larger overhead than that by hardware units, an IPC on software emulators is lower than that on real processors. In this paper, we propose a new method for executing many kinds of traditional instruction sets. The method decomposes them into internal instructions based on information from memory. The memory-based decoder decomposes target CISC instructions into simple instructions. We evaluate an instruction decomposition method and the memory-based decoders. The average IPC of a memory-based decoder is 0.53, which is six times higher than that on JIT type software emulators. The total memory size of the decoder is 98 KB. The chip area of the processor that has the decoder using RAM is 1.36 times larger than that with a hardwired decoder. Therefore, we conclude that the proposed method provides a good tradeoff between chip area and performance.
Information Technology Governance in Practice: A Project Management Office's Use of Early Risk Assessment as a Relational Mechanism

This paper compares implementation frameworks for Information Technology IT governance and functions of a Project Management Office PMO. While there are commonalities, the relational mechanisms called for in IT governance frameworks are omitted from the PMO functions. The authors provide a case study of a PMO at a large municipal government organization where relational mechanisms are incorporated into the risk assessment process through the use of a risk profile spider chart. Drawing conclusions from collaborative practice research, the authors discuss the use and relational aspects of the risk profile spider chart and show how this tool enables boundary spanning between the PMO and other departments by functioning as a boundary object-in-use, increasing the likelihood of buy-in for IT governance decisions. The authors conclude that the tool has potential both as a risk assessment mechanism and a boundary object for building collaboration and thus may be useful for PMOs at other organizations.
Development of Auditory Temporal Resolution in School-Age Children Revealed by Word Recognition in Continuous and Interrupted Noise

Objective: The purpose of the study was to investigate the development of one aspect of auditory temporal resolution in normal-hearing school-age children with word recognition in quiet and in spectrally identical continuous and interrupted noise. Typically, listeners experience a perceptual advantage (i.e., a “release from masking”) in the interrupted noise relative to the continuous noise at equivalent signal-to-noise ratios (S/Ns). Any release from masking observed with children in the interrupted noise compared with the continuous noise at equivalent S/Ns could be interpreted as evidence for acquired temporal resolution ability. Differences in the amount of release from masking in the interrupted noise between children and adults could be interpreted as development of temporal resolution ability, or lack thereof, as revealed by word recognition in noise. It was hypothesized that word recognition performance would be poorer in children than adults; performance differences would be more pronounced with competition; word recognition performance would reach an asymptote to adult levels sooner in quiet than with competing stimuli; children would demonstrate better performance in the interrupted noise relative to the continuous noise (i.e., display a release from masking); and younger children would experience less release from masking compared with older children and adults (i.e., have less developed temporal resolution). Design: Eighty normal-hearing children aged 6 to 15 yr and 16 normal-hearing young adults participated. Word recognition performance with Northwestern University–Children’s Perception of Speech (NU-CHIPs) stimuli was evaluated with an open-set response mode in quiet and in backgrounds of competing continuous steady-state and interrupted noise at S/Ns of 10, 0, −10, and −20 dB. Both noises were essentially identical in their spectral content and differed only in their temporal continuity. Results: Performance was better in the interrupted noise at poorer S/Ns, increased with increasing S/N, and improved with increasing age. Younger listeners were more susceptible to noise. They did not experience an equivalent perceptual advantage (i.e., a release from masking) in the interrupted noise at poorer S/Ns (i.e., <10 dB) and generally required more favorable S/Ns to perform the same as the adult participants. These trends were less pronounced with increasing age. By 8 yr of age, children’s performance in quiet equated that of adult levels, but it did not do so in noise until after 11 yr of age. Conclusions: As revealed by their NU-CHIPs word recognition performance in continuous and interrupted noises, children’s temporal resolving abilities improve in their early school years and reach adult performance levels after 11 yr of age. It was speculated that these changes reflect maturation in their central auditory system.
Mass spectrometry for enzyme assays and inhibitor screening: an emerging application in pharmaceutical research.

Robust methods that monitor enzyme activity and inhibitor potency are crucial to drug discovery and development. Over the past 20 years, mass spectrometric methods have increasingly been used to measure enzyme activity and kinetics. However, for rapid screening of inhibitory compounds, various forms of fluorescence and chemiluminscence readout have continued to dominate the market. As the sensitivity, speed, and miniaturization of mass spectrometry methods continue to advance, opportunities to couple mass spectrometry with screening will continue to come to the forefront. To appreciate the tremendous potential for MS-based screening assays, it becomes necessary to understand the current state of capabilities in this arena. Thus, this review is intended to capture how mass spectrometry for studying enzymes activity has progressed from simple qualitative questions (i.e., is the product detected? ) to quantitative measures of enzyme activity and kinetics and then as a tool for rapidly screening inhibitory compounds as an alternative to current methods of high throughput drug screening.
Do older patients' perceptions of safety highlight barriers that could make their care safer during organisational care transfers?

Background Healthcare is a series of complex, interwoven systems in which any discontinuities of care may affect the safety of patients, who have been reported to perceive safety differently to clinicians. This study aimed to explore patient perceptions of safety and identify how they can be used to construct additional barriers to reduce safety incidents within organisational care transfers, which are known to be high in risk. Design Appreciative Inquiry (AI) methodology was used to develop semi-structured interviews, using the Discover and Dream processes of AI. Fourteen patients (four men, 10 women; average age 76.2 years) were purposively recruited from NHS community care teams, social care homes and private nursing homes based on their experience of going through organisational care transfers. Thematic analysis was used to highlight key themes, which participants verified. Findings Communication, responsiveness and avoidance of traditional safety risks were identified as being important for patients to feel safe. Communication and responsiveness were mapped onto the Swiss-Cheese model of safety, presenting two new barriers to safety incidents. Traditional risks and the role of trust are discussed in relation to patients feeling safe. Conclusion Perceptions of safety such as communication and responsiveness were similar to those found in previous studies. Mapping these perceptions onto the Swiss-Cheese model of safety identifies how further defences, barriers and safeguards can be constructed to make people feel safer by reinforcing communication and responsiveness. Traditional risks are widely published, but the identification by patients reinforces the role they can play in identifying and reporting these risks.
Metal uptake by Lolium perenne in contaminated soils using a four‐step approach

—Most research dealing with soil (solution) speciation and metal uptake by plants has focused on the relationships between a certain bioavailable fraction in the soil and metal uptake by aboveground parts of the plants. Here, a new approach to interpretation of metal uptake is presented that considers four steps: First, the metal concentration in the soil solution is related to the total metal content of the soil. Second, the metal adsorption to the root surface is related to the metal concentration in the soil solution. Third, the metal content in the roots is related to the adsorption of metal ions to the root surface. Fourth, the metal content in the shoots is related to the metal content in the roots. For grass grown on 10 different soils, it is shown that the metal adsorption to the root surface is pH‐dependently related to the free or total metal concentration in the soil solution. The metal content in the roots depends linearly on the metal adsorption at the root surface, whereas the metal content in the shoots depends on the metal content in the roots, either linearly (Zn) or reaching a maximum (Cu, Pb, and Cd). For the Ni content in the shoots as a function of the root content, the relation is pH dependent, probably because of the competition effects of Ca. The pH of the soil has to be taken into account when CaCl2 extractions are used as a basis for risk assessment toward plants.
Spontaneous Perforation of the Bile Duct in Infancy and Childhood: A Systematic Review

CASE 1 A 3-month-old boy presented with a history of jaundice, abdominal distension, vomiting, pale stools, and failure to thrive. On examination, the child was jaundiced but not unwell. The abdomen was distended with the presence of massive ascites. Bilateral hydroceles were evident. Serum liver enzymes were within normal limits. Plain abdominal film showed a ground glass appearance. Abdominal ultrasound scan (USS) showed normal liver and gallbladder with no dilatation of the intrahepatic bile ducts. No mass was detected. Radionuclide scanning demonstrated prompt visualisation of the liver and gallbladder, followed by visualisation of the CBD that looked slightly dilated. The tracer was found to be leaking into the peritoneal cavity, and there was no tracer in the intestines even at 24 hours (Fig. 1). Ascitic aspiration revealed yellow-coloured fluid. With the diagnosis of spontaneous biliary perforation in mind, a laparotomy was performed. There was a thinwalled pseudocyst at the porta hepatis. Intraoperative cholangiogram through the gallbladder showed extravasation of contrast from the CBD. A small perforation was found on the anterior wall of the CBD at the junction with the cystic duct. There was no distal obstruction. A cholecystectomy was performed and a size 8F T tube was placed into the perforation and the perforation closed around this. An external drain was left in the area of the pseudocyst. The T tube was removed once it had stopped draining and the external drained removed 2 days later. This patient was alive and well 1 year postoperatively.
Concordance of murine quantitative trait loci for salt-induced hypertension with rat and human loci.

To investigate the genetic control of salt-induced hypertension, we performed a quantitative trait locus analysis on male mice from a reciprocal backcross between the salt-sensitive C57BL/6J and the normotensive A/J inbred mouse strains after they were provided with water containing 1% salt for 2 weeks. Genome-wide scans performed on these mice and analyzed with a combination of conventional marker-based regressions and a novel simultaneous search for pairs revealed six significant quantitative trait loci associated with salt-induced blood pressure, two of which were interacting loci. These six loci, named Bpq1-6 for blood pressure quantitative trait loci, mapped to D1Mit334, D1Mit14, D4Mit164, D5Mit31, D6Mit15, and D15Mit13. Furthermore, five of these six loci were concordant with hypertension loci in rats, and four were concordant with hypertension loci in humans, suggesting that quantitative trait loci mapping in model organisms can be used to guide the search for human blood pressure genes.
LP norm SAR tomography by iteratively reweighted least square: First results

Synthetic aperture radar tomography (TomoSAR) estimates the scene reflectivity along range, azimuth and elevation directions. Even if many works in recent literature deal with this topic, TomoSAR imaging remains a not easy procedure. In this work, the possibility to improve quality of imaging by a priori information is investigated experimentally; in particular we focus on urban scenario where targets of interest are point-like and radiometrically strong. Accordingly, we look for a sparse reflectivity function; this can be obtained minimizing the solution in an arbitrary Lp norm using the It-eratively Reweighted Least Square (IRLS) algorithm. Based on an experimental comparison among different choices for p, the conclusion drawn is that the usual choice p = 1 is the best trade-off between resolution and robustness to noise. Therefore, L1 norm minimization by IRLS has been exploited to perform CS TomoSAR on real data, and we report in this paper first results obtained using COSMO-SKyMed data acquired over an area in Milan, Italy.
Role of Ca 2 (cid:2) /Calmodulin-Dependent Protein Kinase Kinase in Adrenal Aldosterone Production

There is considerable evidence supporting the role of calcium signaling in adrenal regulation of both aldosterone synthase (CYP11B2) and aldosterone production. However, there have been no studies that investigated the role played by the Ca 2 (cid:2) /calmodulin-dependent protein kinase kinase (CaMKK) in adrenal cells. In this study we investigated the role of CaMKK in adrenal cell aldosterone production. To determine the role of CaMKK, we used a selective CaMKK inhibitor (STO-609) in the HAC15 human adrenal cell line. Cells were treated with angiotensin II (Ang II) or K (cid:2) and evaluated for the expression of steroidogenic acute regulatory protein and CYP11B2 (mRNA/protein) as well as aldosterone production. We also transduced HAC15 cells with lentiviral short hairpin RNAs of CaMKK1 and CaMKK2 to determine which CaMKK plays a more important role in adrenal cell regulation of the calcium signaling cascade. The CaMKK inhibitor, STO-609, decreased aldosterone production in cells treated with Ang II or K (cid:2) in a dose-dependent manner. STO-609 (20 (cid:2) M) also inhibited steroidogenic acute regulatory protein and CYP11B2 mRNA/protein induction. CaMKK2 knockdown cells showed significant reduction of CYP11B2 mRNA induction and aldosterone production in cells treated with Ang II, although there was no obvious effect in CaMKK1 knockdown cells. In immunohistochemical analysis, CaMKK2 protein was highly expressed in human adrenal zona glomerulosa with lower expression in the zona fasciculata. In conclusion, the present study suggests that CaMKK2 plays a pivotal role in the calcium signaling cascade regulating adrenal