Miracle-dz/UniFAR-FTUs huggingface dataset:
A Visual Analytics Tool for Experimental Evaluation

Information Retrieval is a research field strongly rooted in experimentation. Indeed, measuring is a key to scientific progress. Multilingual and multimedia information access systems, such as search engines, are increasingly complex: they need to satisfy diverse user needs and support challenging tasks. It is therefore fundamental to provide automated tools to examine system behaviour, both visually and analytically. This paper provides an analytical model for examining performances of IR systems, based on the discounted cumulative gain family of metrics, and visualization for interacting and exploring the performances of the system under examination.
Mechanism of RAD51-Dependent DNA Interstrand Cross-Link Repair

An in vitro system reveals the steps involved in repairing covalent links between DNA strands of the double helix. DNA interstrand cross-links (ICLs) are toxic DNA lesions whose repair in S phase of eukaryotic cells is incompletely understood. In Xenopus egg extracts, ICL repair is initiated when two replication forks converge on the lesion. Dual incisions then create a DNA double-strand break (DSB) in one sister chromatid, whereas lesion bypass restores the other sister. We report that the broken sister chromatid is repaired via RAD51-dependent strand invasion into the regenerated sister. Recombination acts downstream of FANCI-FANCD2, yet RAD51 binds ICL-stalled replication forks independently of FANCI-FANCD2 and before DSB formation. Our results elucidate the functional link between the Fanconi anemia pathway and the recombination machinery during ICL repair. In addition, they demonstrate the complete repair of a DSB via homologous recombination in vitro.
Cancer cell micronucleus: an update on clinical and diagnostic applications

Micronucleus (MN) is the small nucleus that forms whenever a chromosome or its fragment is not incorporated into one of the daughter nuclei during cell division. Any form of genotoxic stress due to extraneous or internal factors leads to formation of a MN, which serves as an indicator of chromosomal instability. Chromosomal damage and formation of MN are believed to play a significant role in the pathogenesis of many malignancies. Studies have shown that MN assay can be used as a tool for risk prediction, screening, diagnosis, prognosis and as a treatment‐response indicator in cancers. With the advancements in technology, greater details are becoming available regarding the molecular events in carcinogenesis. The micronuclei (MNi) in the cancer cells are now being used as tools to understand the pathogenetics of the malignancies. However, despite large number of studies on MNi in lymphocytes or exfoliated cells of cancer patients, the data regarding a cancer cell MN remain scarce. This review article tries to unleash some of the mysteries related to the formation of MN inside the cancer cell. Also, it discusses the possible effects and the events post MN formation in the cancer cell.
Dynamically stable motion planning of wheeled robots for heavy object manipulation

Heavy object manipulation by wheeled mobile manipulators (WMM) may lead to serious consequences such as postural instability, and this necessitates dynamically stable planning based on systematic analysis to better predict and eliminate the possibility of toppling down. Although the problem of stable planning has been extensively examined in the context of humanoid robotics, fewer research has been devoted to that in the field of WMMs. In the present study, this challenging issue is investigated for WMMs during heavy object manipulation tasks. It is assumed that the initial and final poses of a heavy payload are specified. Based on these known postures of the payload, two proper configurations for robotic system are defined. Then, between these two initial and final poses, appropriate trajectories for multiple robotic arms relative to the moving base are planned without considering the postural stability of the system. Next, motion of the moving base is planned so that the stability of the overall system .
Observation of a Membrane Fusion Intermediate Structure

We report the observation of a phase of phospholipid that contains a structure similar to the commonly postulated interbilayer state that is crucial to membrane fusion. The widely accepted model for membrane fusion suggests that there is an intermediate state in which the two contacting monolayers become continuous via an hourglass-shaped structure called a stalk. Many efforts have been made to estimate the free energy for such a state in order to understand the functionality of membrane fusion proteins and to define key parameters in energy estimates. The observation of the stalk structure supports the stalk hypothesis for membrane fusion and enables the measurement of these parameters experimentally.
Age-related Susceptibility to Induction of Osteochondral and Vascular Lesions by Semicarbazide Hydrochloride in Rats

To compare the susceptibility to toxicity of semicarbazide hydrochloride (SEM-HCl) between young and adult rats, 3- and 20-week-old female SD rats were given a diet containing SEM-HCl at 0, 500, or 1,000 ppm and 0 or 1,000 ppm, respectively, for 4 weeks. Half of the animals were then maintained on basal diet for a further 2 weeks as recovery groups. Only in young rats was deformation of the knee joints as well as thorax and tail observed at 500 and 1,000 ppm. Histopathologically, severe osteochondral lesions, such as disarrangement and thickening of the epiphyseal cartilage and deformation of articular cartilage, were observed, but the severity of these lesions became reduced during the recovery period. In adult rats, osteochondral lesions were relatively mild. Fissures in the cartilage matrix of the tibia were characteristic of adult rats, and in these, reduction of severity was not obvious in the recovery group. In the thoracic aorta, the appearance of elastic laminae was altered only in young rats in both the 4-week treatment and recovery groups. These results suggest that growing animals are more susceptible to toxicity of SEM-HCl than adults are. Effects and the induced lesions link to the developing stage of the target organs.
Brain Diffusivity in Infants With Hypoxic–Ischemic Encephalopathy Following Whole Body Hypothermia

Hypoxic–ischemic encephalopathy is an important cause of neuropsychological deficits. Little is known about brain diffusivity in these infants following cooling and its potential in predicting outcome. Diffusion tensor imaging was applied to 3 groups: (1) three infants with hypoxic–ischemic encephalopathy: cooled; (2) three infants with hypoxic–ischemic encephalopathy: noncooled; and (3) four controls. Diffusivity values at the corticospinal tract, thalamus, and putamen were correlated with Apgar scores and early neurodevelopmental outcome. While cooled infants exhibited lower Apgar scores than noncooled infants, their developmental scores at a mean age of 8 months were higher. All groups differed in their diffusivity values with the cooled infants showing better values compared with the noncooled, correlating with early neurodevelopmental outcome. These preliminary results indicate that diffusion tensor imaging performed at an early age in infants with hypoxic–ischemic encephalopathy may forecast clinical outcome and support the neuroprotective effect of hypothermia treatment.
A localized multimeric anchor attaches the Caulobacter holdfast to the cell pole

Caulobacter crescentus attachment is mediated by the holdfast, a complex of polysaccharide anchored to the cell by HfaA, HfaB and HfaD. We show that all three proteins are surface exposed outer membrane (OM) proteins. HfaA is similar to fimbrial proteins and assembles into a high molecular weight (HMW) form requiring HfaD, but not holdfast polysaccharide. The HfaD HMW form is dependent on HfaA but not on holdfast polysaccharide. We show that HfaA and HfaD form homomultimers and that they require HfaB for stability and OM translocation. All three proteins localize to the late pre‐divisional flagellar pole, remain at this pole in swarmer cells, and localize at the stalk tip after the stalk is synthesized at the same pole. Hfa protein localization requires the holdfast polysaccharide secretion proteins and the polar localization factor PodJ. An hfaB mutant is much more severely deficient in adherence and holdfast attachment than hfaA and hfaD mutants. An hfaA, hfaD double mutant phenocopies either single mutant, suggesting that HfaB is involved in holdfast attachment beyond secretion of HfaA and HfaD. We hypothesize that HfaB secretes HfaA and HfaD across the outer membrane, and the three proteins form a complex anchoring the holdfast to the stalk.
La parole spontanée : transcription et traitement [Processing and transcribing spontaneous speech]

This paper deals with spontaneous speech, considering first its specificities, and then its transcription - both diachronically and synchronically. The paper continues by listing the main problems spontaneous speech causes to automatic speech recognition systems, which were identified through several experiments. It ends by suggesting some optimizations to help solve these problems.
The nucleotide sequence of the ribosomal protein L14 gene of Xenopus laevis.

nucleotide L14 SEQUENCE ORIGIN The X.laevis L14 gene, coding for the protein L14 of the large ribosomal subunit, was isolated from a genomic library in Charon 4 and subcloned in pBR322. Capsite was determined by primer extension and Si map-ping (1). Sequencing was according to Maxam and Gilbert (2).
Rank‐dependent grooming patterns and cortisol alleviation in Barbary macaques

Flexibly adapting social behavior to social and environmental challenges helps to alleviate glucocorticoid (GC) levels, which may have positive fitness implications for an individual. For primates, the predominant social behavior is grooming. Giving grooming to others is particularly efficient in terms of GC mitigation. However, grooming is confined by certain limitations such as time constraints or restricted access to other group members. For instance, dominance hierarchies may impact grooming partner availability in primate societies. Consequently specific grooming patterns emerge. In despotic species focusing grooming activity on preferred social partners significantly ameliorates GC levels in females of all ranks. In this study we investigated grooming patterns and GC management in Barbary macaques, a comparably relaxed species. We monitored changes in grooming behavior and cortisol (C) for females of different ranks. Our results show that the C‐amelioration associated with different grooming patterns had a gradual connection with dominance hierarchy: while higher‐ranking individuals showed lowest urinary C measures when they focused their grooming on selected partners within their social network, lower‐ranking individuals expressed lowest C levels when dispersing their grooming activity evenly across their social partners. We argue that the relatively relaxed social style of Barbary macaque societies allows individuals to flexibly adapt grooming patterns, which is associated with rank‐specific GC management. Am. J. Primatol. 77:688–700, 2015. © 2015 Wiley Periodicals, Inc.
Metabolic flux analysis of the phenylpropanoid pathway in wound-healing potato tuber tissue using stable isotope-labeled tracer and LC-MS spectroscopy.

The metabolic flux of two phenylpropanoid metabolites, N-p-coumaroyloctopamine (p-CO) and chlorogenic acid (CGA), in the wound-healing potato tuber tissue was quantitatively analyzed by a newly developed method based upon the tracer experiment using stable isotope-labeled compounds and LC-MS. Tuber disks were treated with aqueous solution of L-phenyl-d(5)-alanine, and the change in the ratio of stable isotope-labeled compound to non-labeled (isotope abundance) was monitored for p-CO and CGA in the tissue extract by LC-MS. The time-dependent change in the isotope abundance of each metabolite was fitted to an equation that was derived from the formation and conversion kinetics of each compound. Good correlations were obtained between the observed and calculated isotope abundances for both p-CO and CGA. The rates of p-CO formation and conversion (i.e. fluxes) were 1.15 and 0.96 nmol (g FW)(-1) h(-1), respectively, and for CGA, the rates 4.63 and 0.42 nmol (g FW)(-1) h(-1), respectively. This analysis enabled a direct comparison of the biosynthetic activity between these two compounds.
Early precut sphincterotomy for difficult biliary access to reduce post-ERCP pancreatitis: a randomized trial

Background and study aim: Precut sphincterotomy is a technique usually employed for difficult biliary cannulation during endoscopic retrograde cholangiopancreatography (ERCP) for the treatment of bile duct disease. It is a validated risk factor for post-ERCP pancreatitis (PEP), but it is not clear whether the risk is related to the technique itself or to the repeated biliary cannulation attempts preceding it. The primary aim of the study was to assess the incidence of PEP in early precut compared with the standard technique in patients with difficult biliary cannulation. Secondary aims were to compare complications and cannulation success. Patients and methods: In this prospective, multicenter, randomized, clinical trial, patients who were referred for therapeutic biliary ERCP and difficult biliary cannulation were randomized to early precut (Group A) or repeated papillary cannulation attempts followed, in cases of failure, by late precut (Group B). PEP was defined as the onset of upper abdominal pain associated with an elevation in serum pancreatic enzymes of at least three times the normal level at more than 24 hours after the procedure. No rectal indomethacin or diclofenac was used for prevention of PEP. Results: A total of 375 patients were enrolled. PEP developed in 10 of the 185 patients (5.4 %) in Group A and 23 of the 190 (12.1 %) in Group B (odds ratio [OR] 0.35; 95 % confidence interval [CI] 0.16 – 0.78). The incidence of PEP was significantly lower in the early precut group (10/185, 5.4 %) than in the delayed precut subgroup (19/135 [14.1 %]; OR 0.42, 95 %CI 0.17 – 1.07). There were no differences in biliary cannulation success rates, bleeding, perforation, and cholangitis. Conclusions: In patients with difficult biliary cannulation, early precut is an effective technique and can significantly reduce the incidence of PEP. Repeated biliary cannulation attempts are a real risk factor for this complication.
The Melbourne Consensus Statement on the early detection of prostate cancer

Various conflicting guidelines and recommendations about prostate cancer screening and early detection have left both clinicians and their patients quite confused. At the Prostate Cancer World Congress held in Melbourne in August 2013, a multidisciplinary group of the world's leading experts in this area gathered together and generated this set of consensus statements to bring some clarity to this confusion. The five consensus statements provide clear guidance for clinicians counselling their patients about the early detection of prostate cancer.
Accuracy-improved through-silicon-via model using conformal mapping technique

In this paper, the effects of slow wave and dielectric quasi-TEM modes in through-silicon via (TSV) are analyzed by using the currently used TSV model. By the E-field plot, if pitch-to-diameter ratio is small in TSV structure, it is found out that some electrical behaviour of the TSVs is not well characterized by conventional model. This paper proposes a general and analytic model for the electrical modeling of through-silicon via (TSV) based on the conformal mapping method to modify the conventional model in admittance (CG) parts. With the improved model, the electrical performance of the modified model agrees very well with full-wave simulation up to 40GHz for small normalized pitch TSV.
Concentration fluctuations and dilution in aquifers

The concentration of solute undergoing advection and local dispersion in a random hydraulic conductivity field is analyzed to quantify its variability and dilution. Detailed numerical evaluations of the concentration variance σc2 are compared to an approximate analytical description, which is based on a characteristic variance residence time (VRT), over which local dispersion destroys concentration fluctuations, and effective dispersion coefficients that quantify solute spreading rates. Key features of the analytical description for a finite size impulse input of solute are (1) initially, the concentration fields become more irregular with time, i.e., coefficient of variation, CV=σc/〈c〉, increases with time (〈c〉 being the mean concentration); (2) owing to the action of local dispersion, at large times (t > VRT), σc2 is a linear combination of 〈c〉2 and (∂〈c〉/∂xi)2, and the CV decreases with time (at the center, CV ≅ (N)1/2 VRT/t, N being the macroscopic dimensionality of the plume); (3) at early time, dilution and spreading can be severely disconnected; however, at large time the volume occupied by solute approaches that apparent from its spatial second moments; and (4) in contrast to the advection‐local dispersion case, under advection alone, the CV grows unboundedly with time (at the center, CV ∝ tN/4), and spatial second moment is increasingly disconnected from dilution, as time progresses. The predicted large time evolution of dilution and concentration fluctuation measures is observed in the numerical simulations.
Synovial Fluid Cell Count for Diagnosis of Chronic Periprosthetic Hip Infection

Background: There is a paucity of data regarding the threshold of synovial fluid white blood-cell (WBC) count and polymorphonuclear cell (neutrophil) percentage of the WBC count (PMN%) for the diagnosis of chronic periprosthetic joint infection (PJI) after total hip arthroplasty. Despite this, many organizations have provided guidelines for the diagnosis of PJI that include synovial fluid WBC count and PMN%. We attempted to define a threshold for synovial fluid WBC count and PMN% for the diagnosis of chronic PJI of the hip using a uniform definition of PJI and to investigate any variations in the calculated thresholds among institutions. Methods: From 4 academic institutions, we formed a cohort of 453 patients with hip synovial fluid cell count analysis as part of the work-up for revision total hip arthroplasty. Using the definition of PJI from the Musculoskeletal Infection Society (MSIS), 374 joints were diagnosed as aseptic and 79, as septic. Intraoperative aspirations were performed as routine practice, regardless of the suspicion for infection, in 327 (72%) of the patients. Using receiver operating characteristic curves, the optimal threshold values for synovial WBC count and PMN% were identified. Results: For the diagnosis of chronic PJI of the hip, the threshold for the overall cohort was 3,966 cells/&mgr;L for WBC count and 80% for PMN%. Despite the high predictive accuracy for the cohort, there was notable institutional variation in fluid WBC count and PMN%. Furthermore, the rate of PJI was 14% (4 of 28) for patients with a WBC count of 3,000 to 5,000 cells/&mgr;L compared with 91% (20 of 22) for patients with a WBC count of >50,000 cells/&mgr;L. Similarly, the rate of PJI was 29% (14 of 49) for patients with a PMN% of 75% to 85% compared with 69% (33 of 48) for patients with a PMN% of >95%. Conclusions: Using the MSIS criteria, the optimal synovial fluid WBC count and PMN% to diagnose chronic PJI in the hip is closer to thresholds for the knee than those previously reported for the hip. This study validates the diagnostic utility of synovial fluid analysis for the diagnosis of periprosthetic hip infection; however, we also identified a clinically important “gray area” around the threshold for which the presence of PJI may be unclear. Level of Evidence: Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Modification of the effects of atropine on human heart rate by pralidoxime

Eight subiects each received atropine and pralidoxime alone, simultaneously but separately, and also mixed in the same iniection. Heart rates were counted as an indication of absorption of atropine. When the drugs were mixed before iniection, the heart rate response had a significantly longer latent period than that when they were given simultaneously but separately. The addition of pralidoxime to atropine somehow impedes the action of atropine.
Effects and mechanism of suberoylanilide hydroxamic acid on the proliferation and apoptosis of human hepatoma cell line Bel-7402.

PURPOSE To investigate the effects and mechanism of suberoylanilide hydroxamic acid (SAHA) on the proliferation and apoptosis of human hepatoma cell line Bel-7402. METHODS SAHA treatment and control groups were designed in this study. To observe the morphological characteristics and the inhibition of cell proliferation, we conducted confocal microscopy and methyl thiazolyl tetrazolium (MTT) assay, respectively. Changes in cell apoptosis and cell cycle were then determined by flow cytometry. Real-time polymerase chain reaction (RT-PCR) was also conducted to detect the mRNA expressions of p53, bcl-2 and bax genes. Caspase-3 protein activity was determined by spectrophotometry. RESULTS Cell proliferation in the SAHA treatment group could be inhibited in a time- and dose-dependent manner. FCM analysis showed that the early apoptosis rate in the SAHA treatment group increased significantly. Furthermore, cell cycle was arrested at the S phase. RT-PCR assay confirmed that SAHA could upregulate the mRNA expressions of p53 and bax genes. By comparison, SAHA could downregulate the mRNA expression of bcl-2. SAHA induced apoptosis by activating the caspase-3 pathway. CONCLUSION SAHA inhibited cell proliferation and promoted human hepatoma Bel-7402 cell apoptosis by affecting caspase-3 protein activity and mRNA expressions of p53, bcl-2 and bax genes.
Web-based knowledge intensive intelligent support for robot family design

This paper presents an approach to the design of robotic systems from the perspectives of product family design and knowledge support, i.e., a platform based robot family design using a knowledge intensive support paradigm. The high-level information and knowledge modeling issues regarding the design of families of robotic systems are addressed. A module-based integrated robot family design scheme is proposed with knowledge support for task or customer requirement modeling, robot architecture modeling, robot platform establishment, robot family generation, and robot assessment. The issues and requirements, related to the development of knowledge intensive support framework and system for module-based robot family design, are also addressed. The developed web-based prototype system can provide support for robot/family customization design over the Internet. Finally, the design cases are provided.