Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulation of motoneuron morphology in three dimensions. I. Building individual dendritic trees

We have developed a computational method that accurately reproduces the three‐dimensional (3D) morphology of individual dendritic trees of six cat alpha motoneurons. The first step was simulation of trees with straight branches based on the branch lengths and topology of actual trees. A second step introduced the meandering, or wandering, trajectories observed in natural dendritic branches into the straight‐branch tree simulations. These two steps each required only two parameters, one extracted from the data on actual motoneuron dendrites and the other adjusted by comparing simulated and observed trees, using measurements that were independent of the model specifications (i.e., emergent properties). The results suggest that: 1) there is a somatofugal “tropism” (a bias introduced by the environment that affects the trajectory of dendritic branches) that tends to constrain the lateral expansion of alpha motoneuron dendrites; and 2) that most of the meandering of natural dendritic branches can be described by assuming that they are fractal objects with an average fractal dimension D of about 1.05. When analyzed in the same way, the dendrites of gamma motoneurons showed no evidence of a similar tropism, although they had the same fractal dimension of branch meandering. J. Comp. Neurol. 503:685–700, 2007. Published 2007 Wiley‐Liss, Inc.
Long term lymphocyte reconstitution after alemtuzumab treatment of multiple sclerosis

Background Alemtuzumab is a lymphocyte depleting monoclonal antibody that has demonstrated superior efficacy over interferon β-1a for relapsing–remitting multiple sclerosis (MS), and is currently under investigation in phase 3 trials. One unresolved issue is the duration and significance of the lymphopenia induced. The long term effects on lymphocyte reconstitution of a single course, and the consequences that this has on disability, morbidity, mortality and autoimmunity, were examined. Methods The lymphocyte reconstitution (n=36; 384 person years) and crude safety data (n=37; 447 person years) are reported for the first patients with progressive MS to receive alemtuzumab (1991–1997). Reconstitution time was expressed as a geometric mean or, when a non-negligible number of individuals failed to recover, as a median using survival analysis. Results Geometric mean recovery time (GMRT) of total lymphocyte counts to the lower limit of the normal range (LLN; ≥1.0×109 cells/l) was 12.7 months (95% CI 8.8 to 18.2 months). For B cells, GMRT to LLN (≥0.1×109/l) was 7.1 months (95% CI 5.3 to 9.5); median recovery times for CD8 (LLN ≥0.2×109 cells/l) and CD4 lymphocytes (LLN ≥0.4×109 cells/l) were 20 months and 35 months, respectively. However, CD8 and CD4 counts recovered to baseline levels in only 30% and 21% of patients, respectively. No infective safety concerns arose during 447 person years of follow-up. Conclusions Lymphocyte counts recovered to LLN after a single course of alemtuzumab in approximately 8 months (B cells) and 3 years (T cell subsets), but usually did not recover to baseline values. However, this long lasting lymphopenia in patients with a previously normal immune system was not associated with an increased risk of serious opportunistic infection.
RF Pulse Toolkit: Application Specific Design

The most simple type of excitation pulse is known as a ‘hard’ pulse, and is illustrated in Fig. 1a. A hard pulse has constant magnitude and phase. Because MRI systems generate RF pulses using sample-and-hold DAC circuitry, all RF pulses can be accurately modeled as a series of short hard pulses of varying amplitude and phase. Figure 1b shows how magnetization rotates about a hard pulse, in a frame rotating about the z-axis at the Larmor frequency. In that figure, the pulse is applied along the x-axis, so that magnetization is rotated in the y-z plane. The flip angle excited by a hard pulse is simply its duration T , multiplied by its magnitude |B1| and the gyromagnetic ratio γ:
Hybrid Discrete Singular Convolution-Method of Moments Analysis of a 2-D Transverse Magnetic Reverberation Chamber

In this paper, a new hybrid technique combining the discrete singular convolution (DSC) method and the method of moments (MoM) is proposed for efficient analysis of a 2-D transverse magnetic reverberation chamber. The metallic stirrer is viewed as a current sheet along whose surface the tangential electric field is forced to zero. The DSC method is used to model the cavity excited by the original source plus the current sheet, which are expressed on the grids of the DSC method using the regularization technique. The MoM is used to enforce the boundary condition along the stirrer. Solutions from the aforementioned two steps are coupled together with the aid of the equivalence principle. The validity and advantage of the proposed hybrid technique is shown through comparisons with results from alternative methods. Taking advantage of the high efficiency of the DSC method, the new hybrid technique is shown to be a lot more efficient than a pure MoM with approximately the same memory cost.
Use of the Brief Psychiatric Rating Scale as a Predictor of Psychiatric Admission for Non-Suicidal Patients

Objective: We hypothesized that a systematic determination of symptom severity would predict psychiatric admission for non-suicidal patients referred for a psychiatric evaluation in an urban emergency department (ED) setting. Method: In a pilot study involving consecutive patients referred for a psychiatric evaluation in an urban ED, symptom severity was quantified using the Brief Psychiatric Rating Scale (BPRS). The BPRS scores of all non-suicidal patients were subjected to receiver operator characteristic (ROC) curve analysis to determine the sensitivity, specificity, and optimal cutoff score of the BPRS in predicting admission for non-suicidal patients. Results: A BPRS cutoff score of 39 had a sensitivity of 85.71 percent and a specificity of 86.11 percent. The area under the ROC curve was . 8671 (Somer's D = .7342) and the standard error of the curve was . 1124. The cutoff score of 39 correctly identified six of seven non-suicidal patients who were hospitalized. Conclusions: It is anticipated that use of the BPRS in the ED will be further refined when a larger patient sample is studied. Potentially, a subset of BPRS items could be identified which would be more sensitive in predicting admission than the full BPRS and increase the overall efficiency of administering the BPRS in the ED.
Optical Coherence Tomography in Glaucoma

The optic disk and the RNFL are the principal sites of apparent glaucomatous damage which precedes glaucomatous visual field alterations. RNFL defects are known to precede detection of visual field defects by approximately 6 years. Accurate early detection and monitoring of ONH and RNFL defects has become the prime focus of effective management of glaucoma. Optical coherence tomography employs low-coherence interferometry to obtain cross-sectional images of the ocular tissues. This review attempts to critically analyse the applications of both, anterior and posterior segment OCT in glaucoma management.
An inherently monotonic 12 bit DAC

Describes a 12 bit DAC which uses diffused resistors and requires no trimming to guarantee monotonicity for all grades over the temperature range. The segmented ladder design, departing from the traditional R-2R approach used in virtually all high-speed high resolution converters, provides inherent monotonicity and differential linearity as high as 13 bits. Also afforded is a more uniform step size over the temperature range than the trimmed 12 bit converters. The only critical resistor matching occurs at the major carries or midpoints of each of the eight segments and the tolerances are equivalent to that of a 9 bit DAC, or eight times lower than the R-2H approach. In essence, the problem has been divided into eight separate problems, each with tolerances eight times lower than that of a 12 bit DAC. The converter has been found to be immune to variations in temperature, time, process, and mechanical stress. The circuit also features differential high compliance current outputs, wide supply range, and a multiplying input.
Polyol pathway along the bovine epididymis

During the epididymal transit, male gametes acquire new surface proteins necessary for their fertilizing ability. We have previously shown that membranous vesicles, called epididymosomes, interact with sperm surface within the epididymal fluid allowing transfer of some proteins to different subcellular compartments of spermatozoa. We previously showed that one of the major proteins associated with epididymosomes was an aldose reductase (gene: AKR1B5) and confirmed that aldose reductase is located in the epithelial cells bordering the intraluminal compartment of the epididymis. The present study shows that cytosolic aldose reductase activity was maximal in the proximal and middle segments of the epididymis and decreased in the distal epididymis. Western and Northern blot analysis confirmed the distribution pattern of aldose reductase and of the encoding mRNA. The optimal pH of epididymal aldose reductase was 6.0–6.5 when glucose was used as a substrate; this corresponds to the pH of the intraluminal epididymal fluid. In order to evaluate the possible involvement of sorbitol in sperm physiology, Western blot of tissue homogenates were probed with an anti‐sorbitol dehydrogenase antibody. The amount of enzyme immunodetected was higher in the proximal and distal segments of the epididymis when compared to the amount detectable in the middle segment of the epididymis. Sorbitol dehydrogenase activity as well as the level of the encoding mRNA showed the same pattern of distribution. Furthermore, immunohistological studies using the anti‐sorbitol dehydrogenase revealed that this enzyme was synthesized by the epididymal epithelial cells bordering the intraluminal compartment. Knowing the importance of sorbitol and fructose in sperm metabolism, we hypothesized that the polyol pathway is involved in the modulation of sperm motility within the epididymis. Mol. Reprod. Dev. 69: 448–456, 2004. © 2004 Wiley‐Liss, Inc.
The timing of prophylactic administration of antibiotics and the risk of surgical-wound infection.

BACKGROUND Randomized, controlled trials have shown that prophylactic antibiotics are effective in preventing surgical-wound infections. However, it is uncertain how the timing of antibiotic administration affects the risk of surgical-wound infection in actual clinical practice. METHODS We prospectively monitored the timing of antibiotic prophylaxis and studied the occurrence of surgical-wound infections in 2847 patients undergoing elective clean or "clean-contaminated" surgical procedures at a large community hospital. The administration of antibiotics 2 to 24 hours before the surgical incision was defined as early; that during the 2 hours before the incision, as preoperative; that during the 3 hours after the incision, as perioperative; and that more than 3 but less than 24 hours after the incision, as postoperative. RESULTS Of the 1708 patients who received the prophylactic antibiotics preoperatively, 10 (0.6 percent) subsequently had surgical-wound infections. Of the 282 patients who received the antibiotics perioperatively, 4 (1.4 percent) had such infections (P = 0.12; relative risk as compared with the preoperatively treated group, 2.4; 95 percent confidence interval, 0.9 to 7.9). Of 488 patients who received the antibiotics postoperatively, 16 (3.3 percent) had wound infections (P less than 0.0001; relative risk, 5.8; 95 percent confidence interval, 2.6 to 12.3). Finally, of 369 patients who had antibiotics administered early, 14 (3.8 percent) had wound infections (P less than 0.0001; relative risk, 6.7; 95 percent confidence interval, 2.9 to 14.7). Stepwise logistic-regression analysis confirmed that the administration of antibiotics in the preoperative period was associated with the lowest risk of surgical-wound infection. CONCLUSIONS We conclude that in surgical practice there is considerable variation in the timing of prophylactic administration of antibiotics and that administration in the two hours before surgery reduces the risk of wound infection.
Sjögren’s syndrome and granulomatous panniculitis

An 83‐year‐old Cambodian woman presented with multiple painful erythematous nodules on the lower legs, forearms and wrists. Subsequent history and investigations revealed a granulomatous lobular panniculitis associated with Sjögren’s syndrome. This is a rare cutaneous association of Sjögrens syndrome with only three similar case reports in the literature.
Dicing with Deception: People with Disabilities' Strategies for Managing Safety and Identity Online

The visual anonymity associated with online interaction offers people with disabilities the potential to participate in social interaction beyond the stigma of a disabled identity. In problematizing traditional notions of reality, however, the online medium also has the potential to become a deceptive social space where people with disabilities become victims of malevolent acts. Considering the dilemma surrounding the choice to participate, this study investigates how people with disabilities are managing issues of deception and harm in online contexts. A discursive psychology framework is utilized. The research was conducted in New Zealand where 21 participants with physical and sensory disabilities volunteered to participate in an online interview. Two different repertoires enabled people with disabilities to manage the dilemma of engaging in a medium where there is potential for benefit and harm. A keeping safe repertoire deployed three safety strategies to protect participants from deceptive acts. Data from several participants was also categorized under a qualified deception repertoire. This allowed participants to access new subjective experiences outside of a disabled identity and to extend their online engagement beyond keeping safe. Both repertoires maintained participants' integrity as online users.
Serial Diffusion Tensor Imaging Detects White Matter Changes That Correlate with Motor Outcome in Premature Infants

The objective of the study was to assess predictive value of serial diffusion tensor MRI (DTI) for the white matter injury and neurodevelopmental outcome in a cohort of premature infants. Twenty-four infants less than 32 weeks’ gestation were stratified to a control group (n = 11), mild brain injury with grades 1–2 of intraventricular hemorrhage (n = 6) and severe brain injury with grades 3–4 intraventricular hemorrhage (n = 4). Serial DTI studies were performed at around 30 and 36 weeks’ gestation. Fractional anisotropy (FA) and apparent diffusion coefficient were calculated. Twelve infants were followed up for developmental outcome. Developmental testing was performed with the Bayley Scales of Infant Development to obtain psychomotor index (Performance Developmental Index). Apparent diffusion coefficient was higher in the severe injury group at the second MRI in the central and occipital white matter, and corona radiata; FA was lower in optic radiation compared to controls. Performance Developmental Indexscore correlated with FA on the scan taken at the 30th week and inversely with the change of FA between scans in internal capsule and occipital white matter. A low value of FA at 30 weeks and a higher change of FA predicted less favorable motor outcome at 2 years and suggests that early subtle white matter injury can be detected in premature infants even without obvious signs of injury.
Mesures de la qualité des systèmes de recherche d'information

In this paper we review approaches for evaluating information retrieval systems us- ing test collections. We first give the definition of a test collection and present the main metrics used in literature to evaluate systems. We then show, thanks to three examples (search results clustering, automatic summarization and image retrieval), the variety of the existing evaluation frameworks. RESUME. L'objectif de cet article est de presenter un panorama de l'evaluation des systemes de recherche d'information se basant sur des collections de reference. Nous detaillons dans un premier temps ce qu'est une collection de reference ainsi que les mesures d'evaluation as- sociees. Nous developpons ensuite les problematiques d'evaluation a travers trois cadres de recherche d'information specifiques: le clustering de documents, le resume automatique et la recherche d'images par l'exemple, et montrons la variete des mesures et collections de reference existantes.
Creating Space for Large Secondary Alcohols by Rational Redesign of Candida antarctica Lipase B

The active site of Candida antarctica lipase B (CALB) hosts the catalytic triad (Ser‐His‐Asp), an oxyanion hole and a stereospecificity pocket. During catalysis, the fast‐reacting enantiomer of secondary alcohols places its medium‐sized substituent in the stereospecificity pocket and its large substituent towards the active‐site entrance. The largest group to fit comfortably in the stereospecificity pocket is ethyl, and this restricts the number of secondary alcohols that are good substrates for CALB. In order to overcome this limitation, the size of the stereospecificity pocket was redesigned by changing Trp104. The substrate specificity of the Trp104Ala mutant compared to that of the wild‐type lipase increased 270 times towards heptan‐4‐ol and 5500 times towards nonan‐5‐ol; this resulted in the high specificity constants 1100 and 830 s−1 M−1, respectively. The substrate selectivity changed over 400 000 times for nonan‐5‐ol over propan‐2‐ol with both Trp104Ala and the Trp104Gln mutations.
Application of nonnegative matrix factorization in recommender systems

Recommender systems actively collect various kinds of data in order to generate their recommendations. Collaborative filtering is based on collecting and analyzing information on users' preferences and estimating what users will like based on their similarity to other users. However, most of current collaborative filtering methods often suffer from two problems: sparsity and scalability. This paper proposes a framework for collaborative filtering by applying nonnegative matrix factorization, which alleviates the problems via matrix factorization. Experimental results on benchmark dataset are presented to show that our method is indeed more tolerant against both sparsity and scalability, and obtains good performance in the meanwhile.
Smarter cut-and-paste for programming text editors

The process of creating software involves many different tools, but the text editor is still one of the most important. Moreover, one of its basic facilities, cut-and-paste, still plays a critical role in enabling simple reuse. In this paper we explore how to improve cut-and-paste within text editors used for programming. We describe how programmers use cut-and-paste for reuse, and suggest the basic underlying principles. We then report on a prototype tool we developed to explore a set of techniques to provide better support for cut-and-paste.
Severe pancytopenia and hemophagocytosis after HHV-8 primary infection in a renal transplant patient successfully treated with foscarnet1

We report the occurrence of human herpesvirus (HHV)-8 primary infection in an adult male kidney recipient. Four months after transplantation, the patient developed visceral Kaposi sarcoma, and 1 month later he presented with progressive and severe peripheral cytopenia, in the presence of a normocellular or hypercellular bone marrow (BM) with hemophagocytosis. HHV-8 was the sole pathogen detected by polymerase chain reaction either in the serum or in the BM. HHV-8 latent nuclear antigen was detected in immature progenitor cells from the BM. Immunosuppressive therapy was reduced, and the patient was treated with foscarnet for 2 weeks, leading to a dramatic normalization of blood cell counts, concomitantly with the disappearance of HHV-8 viremia. At the end of antiviral therapy, the patient received chemotherapy, and Kaposi sarcoma regressed in 2 months. Severe peripheral cytopenia may be a posttransplant complication after HHV-8 infection, for which treatment with foscarnet seems appropriate.
Previous Back Pain and Risk of Developing Back Pain in a Future Pregnancy

Four hundred twenty-nine pregnant women who had back pain before pregnancy and 375 pregnant women with no previous back pain were followed at regular intervals from the 12th week of pregnancy until delivery; back-pain complaints were recorded. Overall, back pain occurred twice as often in the group with a back-pain history (period prevalence) (P < 0.001). The point prevalence of back pain in weeks 12, 24, 30, and 36 was three times higher in the group who had had back pain before pregnancy indicating that pain was not only more prevalent but also lasted longer in that group. Women who had been pregnant previously tended to have an increased risk of back pain, and there was a statistically significant correlation between multiparity and longer periods of back pain (P < 0.001). Young age increased the risk of back pain (P < 0.001). Pain intensity was higher in the younger women during the first part of their pregnancies but not later on (P < 0.05).
Efficient whole-body trajectory optimization using contact constraint relaxation

In this work we present a Trajectory Optimization framework for whole-body motion planning for floating base robots. We demonstrate how the proposed approach can optimize whole body trajectories for most common gaits found in bipeds and quadrupeds. The underlying optimal control problem is solved efficiently using Sequential Linear Quadratic control. In contrast to most previous methods, the proposed approach is fast while still using a full dynamic model. Additionally, the approach is contact model free. Instead contact forces are added to the Optimal Control formulation as additional control inputs and contact constraints are handled using a relaxation approach. In our experiments we demonstrate that, despite this relaxation, our solver resolves constraint violations in only a few iterations. Hardware experiments underline the transferability from simulation to hardware.
Numerical simulation of heat transfer distribution over the surface of internally cooled nozzle guide vane in an annular cascade

A key factor in improving turbine efficiency is higher turbine front temperature. Accurate simulation of the heat transfer coefficient remains a challenge for the prediction of external heat transfer on nozzle guide vane in aero turbine engine. In this paper the shear stress transport turbulence model results are compared against the measured data from Hylton et al., as well as the predictions from a 2-D boundary layer code-STAN5. The heat transfer distribution over the surface of two internally cooled nozzle guide vanes in a transonic annular cascade are investigated. Computational fluid dynamics model of the MARK II vane and the C3X vane were built and several modeling parameters are varied in order to obtain good agreement with the measured data. In addition, the influence of the exit Mach number and the turbulence intensity to the heat transfer of nozzle guide vane were invested.
Toward hybrid simulations for care demand forecasting

Demographic change leads to an increasing demand of health care services. To provide the required services at the right locations, methods for forecasting future demands are needed. The goal of this research is to combine two different simulation techniques to forecast future care service demands. On the one hand, forecasts of demographic change are required. On the other hand, a plausible forecast must account for individual decisions for specific types of care. Thus, the paper outlines an approach to combine statistical micro-simulation of demographic change with agent-based social simulation of individual interactions.