Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Foot and Ankle Immobilization on Leg and Thigh Muscles' Volume and Morphology: A Case Study Using Magnetic Resonance Imaging

Our aim was to determine the time course of any changes in muscle volume and shape in the lower limbs following immobilization. A healthy young woman (29 years) had suffered a fracture of the fifth metatarsal of the right foot. MRI scanning of her right thigh and calf muscles had been performed 1 month before the injury (Pre) during a scan initially planned as a teaching tool, 2 days following a 4‐week immobilization period (Post), and after a 2‐month recovery period (Post+2). The results show muscle volume decrements in the triceps surae (TS), quadriceps (Quad), and hamstring (Ham) of 21.9%, 24.1%, and 6.5%, respectively, between the Pre and Post measurements. At Post+2, the Quad and TS muscle volumes were still 5.2% and 9.5% lower, compared with the Pre data. The Ham muscle volume, however, was 2.7% greater than at the Pre phase. Following recovery, the increase in individual TS muscles volume was limited to both proximal and medial (with respect to the knee joint) segments of the muscles. These results indicate very substantial and rapid losses in muscle volumes, both proximally and distally to the immobilization site. The results also show that recovery is far from complete up to 2 months post cast removal. The results have implications for the requirements for rehabilitation for orthopedic patients. Anat Rec, 2008. © 2008 Wiley‐Liss, Inc.
Fe b 20 05 Parameterizing Quasiperiodicity : Generalized Poisson Summation and Its Application to Modified-Fibonacci Antenna Arrays

The fairly recent discovery of “quasicrystals”, whose X-ray diffraction patterns reveal certain peculiar features which do not conform with spatial periodicity, has motivated studies of the wave-dynamical implications of “aperiodic order”. Within the context of the radiation properties of antenna arrays, an instructive novel (canonical) example of wave interactions with quasiperiodic order is illustrated here for one-dimensional (1-D) array configurations based on the “modifiedFibonacci” sequence, with utilization of a two-scale generalization of the standard Poisson summation formula for periodic arrays. This allows for a “quasi-Floquet” analytic parameterization of the radiated field, which provides instructive insights into some of the basic wave mechanisms associated with quasiperiodic order, highlighting similarities and differences with the periodic case. Examples are shown for quasiperiodic infinite and spatially-truncated arrays, with brief discussion of computational issues and potential applications. ∗V. Galdi, G. Castaldi, V. Pierro and I.M. Pinto are with the Waves Group, Department of Engineering, University of Sannio, I-82100 Benevento, Italy (e-mail: vgaldi@unisannio.it, castaldi@unisannio.it, pierro@unisannio.it, pinto@sa.infn.it). L.B. Felsen is with the Department of Aerospace and Mechanical Engineering and the Department of Electrical and Computer Engineering (part-time), Boston University, Boston, MA 02215 USA. He is also University Professor Emeritus, Polytechnic University, Brooklyn, NY 11201 USA (e-mail: lfelsen@bu.edu).
Pattern and predictors of paradoxical response in patients with peripheral lymph node tuberculosis.

Introduction Many of the patients with lymph node tuberculosis show 'Paradoxical Response" in the form of appearance of new lymph node (LN) or increase in the size of existing LN, development of new disease in other organ and worsening of the disease while on treatment. Reason behind such response in only selective patients is not clearly understood. We evaluated the pattern and predictors for paradoxical response(s) (PR) in patients with peripheral lymph node tuberculosis (TB). Materials and Methods Study included patients aged > 6 years with peripheral lymphadenopathy of tubercular etiology attending a tertiary care hospital from Jan 2010 to Dec 2010. PR in our study was defined as worsening of pre-existing disease or development of new lesions in a patient who has been on anti-TB therapy for at least 2 weeks. Result One hundred ten patients with peripheral lymph node TB were included. Their mean age was 27.5 ± 5 years and 68 (62%) were females. PR occurred in 28 (25%) patients, at a mean onset time of 6 weeks (range 2-12 weeks) after starting anti-TB medication. Four of these 28 patients experienced PR on two occasions. Of these, 22 (79%) patients presented with enlarged lymph nodes only, 8 (29%) with new nodes at same or different site and 2 (7%) with discharging sinus. PR was observed more in younger age group (p> 0.05), female gender (p> 0.05), unilateral lymphadenopathy (p> 0.05) and those with positive AFB on initial examination (p< 0.01). Conclusions Paradoxical response in peripheral lymph node TB is associated with younger age, female gender, unilateral lymphadenopathy and those with positive AFB on initial examination.
Parameters identification of the single-diode model for amorphous photovoltaic panels

The single-diode model, which is widely used for describing the behaviour of the photovoltaic crystalline and multi-crystalline cells, requires to be properly adapted for reproducing the electrical behaviour of amorphous thin film silicon cells. As for the former case, five parameters must be identified for having a good fitting with respect to the experimental measurements or the data reported in the module data sheet. Nevertheless, due to the strong nonlinearity of the model, the fitting procedures suffer from convergency problems and are sensible to the initial guess solution. In this paper a set of explicit equations is developed in order to calculate the approximated values of the five parameters characterising the PV model. These equation have been obtained by extending, to the amorphous case, the procedure already developed for the crystalline single diode model, thus by generalising and reinforcing the validity of that approach. The new formulas have been validated by comparing the results of the proposed approach with the experimental values reported in the data sheet of some amorphous silicon panels.
Elevated levels of expired breath hydrogen peroxide in bronchiectasis.

Airway inflammation is important in the development and progression of many lung diseases, including bronchiectasis. Activation of inflammatory cells such as neutrophils, eosinophils, and macrophages induces a respiratory burst resulting in the production of reactive oxygen species such as hydrogen peroxide (H2O2). We have measured exhaled H2O2 in patients with documented bronchiectasis and investigated whether the concentration of H2O2 is related to the disease severity, as defined by lung function. We also investigated whether the concentrations of expired H2O2 were different in bronchiectatic patients who received inhaled corticosteroids compared with steroid-naïve patients. In 37 patients with bronchiectasis (mean age, 45 +/- 2.5 yr; FEV1, 59 +/- 3% pred), mean H2O2 concentration in exhaled breath condensate was significantly elevated as compared with the values in 25 age-matched (mean age, 42 +/- 2 yr) normal subjects (0.87 +/- 0.01 versus 0.26 +/- 0.04 microM, p < 0.001). There was a significant negative correlation between H2O2 and FEV1 (r = -0.76, p < 0.0001). Patients treated with inhaled corticosteroids had values of H2O2 similar to those of steroid-naïve patients (0.8 +/- 0.1 versus 0.9 +/- 0.1, p > 0.05). We conclude that H2O2 is elevated in exhaled air condensate of patients with bronchiectasis and is correlated with disease severity. Measurement of H2O2 may be used as a simple noninvasive method to monitor airway inflammation and oxidative stress.
Familial temporal lobe epilepsy: A common disorder identified in twins

We describe a new syndrome of familial temporal lobe epilepsy in 38 individuals from 13 unrelated white families. The disorder was first identified in 5 concordant monozygotic twin pairs as part of a large‐scale twin study of epilepsy. When idiopathic partial epilepsy syndromes were excluded, the 5 pairs accounted for 23% of monozygotic pairs with partial epilepsies, and 38% of monozygotic pairs with partial epilepsy and no known etiology. Seizure onset for twin and nontwin subjects usually occurred during adolescence or early adult life. Seizure types were simple partial seizures with psychic or autonomic symptoms, infrequent complex partial seizures, and rare secondarily generalized seizures. Electroencephalograms revealed sparse focal temporal interictal epileptiform discharges in 22% of subjects. Magnetic resonance images appeared normal. Nine affected family members (24%) had not been diagnosed prior to the study. Pedigree analysis suggested autosomal dominant inheritance with age‐dependent penetrance. The estimated segregation ratio was 0.3, indicating an overall penetrance of 60% assuming autosomal dominant inheritance. The mild and often subtle nature of the symptoms in some family members may account for lack of prior recognition of this common familial partial epilepsy. This disorder has similarities to the El mouse, a genetic model of temporal lobe epilepsy with a major gene on mouse chromosome 9, which is homologous with a region on human chromosome 3.
The effects of obesity-associated insulin resistance on mRNA expression of peroxisome proliferator-activated receptor-γ target genes, in dogs

Visceral adipose tissue and skeletal muscle have central roles in determining whole-body insulin sensitivity. The peroxisome proliferator-activated receptor-γ (PPARγ) is a potential mediator of insulin sensitivity. It can directly modulate the expression of genes that are involved in glucose and lipid metabolism, including GLUT4, lipoprotein lipase (LPL) and adipocytokines (leptin and adiponectin). In this study, we aimed to determine the effects of obesity-associated insulin resistance on mRNA expression of PPARγ and its target genes. Dogs were studied when they were lean and at the end of an overfeeding period when they had reached a steady obese state. The use of a sensitive, real-time PCR assay allowed a relative quantification of mRNA expression for PPARγ, LPL, GLUT4, leptin and adiponectin, in adipose tissue and skeletal muscle. In visceral adipose tissue and/or skeletal muscle, mRNA expression of PPARγ, LPL and GLUT4 were at least 2-fold less in obese and insulin-resistant dogs compared with the same animals when they were lean and insulin-sensitive. The mRNA expression and plasma concentration of leptin was increased, whereas the plasma level and mRNA expression of adiponectin was decreased, by obesity. In adipose tissue, PPARγ expression was correlated with leptin and adiponectin. These findings, in an original model of obesity induced by a prolonged period of overfeeding, showed that insulin resistance is associated with a decrease in PPARγ mRNA expression that could dysregulate expression of several genes involved in glucose and lipid metabolism.
Danish retinoblastoma patients 1943–2013 – genetic testing and clinical implications

Abstract Background: In heritable retinoblastoma there is a 50% risk of transmitting the RB1 mutation, and offspring carriers have more than 90% risk of developing retinoblastoma. Today, all newly diagnosed retinoblastoma patients in Denmark are screened for mutations in RB1, as opposed to only a minority of patients diagnosed before DNA testing was offered. Knowledge of heredity increases the chance of early diagnosis in offspring, leading to improved prognosis. We present data from the Danish retinoblastoma patients that emphasize the need for genetic counseling and RB1 screening in all untested retinoblastoma survivors. Material and methods: Data are extracted from The Danish Ocular Oncology Group Database, a national population database containing data on all Danish retinoblastoma patients since 1943. Results: In total 323 retinoblastoma patients have been diagnosed between 1943 and 2013. Since 1963, the rate has been stable around 1 per 14 000 live births with 95% of the patients surviving their retinoblastoma. Stratifying data on the time of diagnosis and status of genetic testing, the number of screened patients gradually increased from 5% in the beginning of the period to 96% in the last five-year period. A cohort of 181 retinoblastoma survivors with sporadic disease (15% heritable) did not receive genetic testing. Since the introduction of routine testing, one of 14 sporadic unilateral patients tested (7%) has been identified with a germline mutation. Before routine testing, five additional sporadic unilateral patients have been identified as heritable. Conclusion: Only a minority of Danish retinoblastoma patients diagnosed before routine genetic testing was offered have been RB1 screened. To counsel the remaining untested patients and their families sufficiently regarding the risk to offspring and elevated risk of second primary cancers, we recommend information and access to genetic counseling and RB1 screening. This has ethical, psychological and possible economic consequences, and should be handled with caution.
Genome analysis popSTR : population-scale detection of STR variants

Motivation: Microsatellites, also known as short tandem repeats (STRs), are tracts of repetitive DNA sequences containing motifs ranging from 2-6 bases. The human reference genome contains approximately 1 million microsatellites, covering almost 1% of the genome (Gymrek et al., 2016). Microsatellite analysis has a wide range of applications, including medical genetics, forensics and construction of genetic genealogy. However, microsatellite variations are rarely considered in wholegenome sequencing studies, in large due to a lack of tools capable of analyzing them (Duitama et al., 2014). Results: Here we present a microsatellite genotyper, optimized for Illumina WGS data, which is both faster and more accurate than other methods previously presented. There are two main ingredients to our improvements. First we reduce the amount of sequencing data necessary for creating microsatellite profiles by using previously aligned sequencing data. Second, we use population information to train microsatellite and individual specific error profiles. By comparing our genotyping results to genotypes generated by capillary electrophoresis we show that our error rates are 50% lower than those of lobSTR, another program specifically developed to determine microsatellite genotypes. Availability: Source code is available on Github: https://github.com/DecodeGenetics/popSTR Contact: snaedis.kristmundsdottir@decode.is, bjarni.halldorsson@decode.is
Induction of inflammatory angiogenesis by monocyte chemoattractant protein‐1

Almost any growth of tumors is to some extent associated with an inflammatory reaction which may be anti‐tumorigenic by acting directly on tumor cells or protumorigenic cells presumably by inducing tumor‐associated angiogenesis. In this study, we have analyzed the angiogenesis‐inducing capacity of monocyte chemoattractant protein‐1 (MCP‐1), a key regulatory molecule of monocyte trafficking to sites of inflammation. MCP‐1 was found to be potently angiogenic when implanted into rabbit cornea, exerting potency similar to the specific angiogenic vascular endothelial growth factor (VEGF)‐A121. MCP‐1‐induced angiogenesis in the cornea is associated with prominent recruitment of macrophages, whereas VEGF‐A121‐induced corneal angiogenesis is devoid of inflammatory cell recruitment. Based on these findings, we studied MCP‐1 expression and macrophage recruitment in human invasive ductal mammary carcinomas in comparison with the physiological angiogenic processes in bovine ovarian corpus luteum. Macrophage recruitment was always associated with MCP‐1 expression. High macrophage counts in mammary tumors corresponded with poor prognosis. In contrast, physiological ovarian angiogenesis was associated with only minimal inflammatory recruitment of macrophages. Our data show that MCP‐1 is an indirect inflammation‐associated inducer of angiogenesis and demonstrate distinct qualitative differences between tumor angiogenesis in human mammary tumors and physiological angiogenesis in the ovary. Int. J. Cancer 82:765–770, 1999. © 1999 Wiley‐Liss, Inc.
A Heuristic For Computing Repeats With A Factor Oracle: Application To Biological Sequences

We present in this article a linear time and space method for the computation of the length of a repeated suffix for each prefix of a given word p . Our method is based on the utilization of the factor oracle of p which is a new and very compact structure introduced in [1], used for representing all the factors of p . We exhibit applications where our method really speeds up the computation of repetitions in words.
Mosaic deletion of Rb arrests rod differentiation and stimulates ectopic synaptogenesis in the mouse retina

The retinoblastoma gene (Rb) regulates neural progenitor cell proliferation and cell fate specification and differentiation. For the developing mouse retina, two distinct functions of Rb have been described: regulation of retinal progenitor cell proliferation and rod photoreceptor development. Cells that would normally become rods fail to mature and remain as immature cells in the outer nuclear layer in the adult. By using Chx10‐Cre;RbLox/− mice, we generated a chimeric retina with alternating apical‐basal stripes of wild‐type and Rb‐deficient tissue. This provides a unique model with which to study synaptogenesis at the outer plexiform layer within regions that lack differentiated rods. In regions where rods failed to differentiate, the outer plexiform layer (OPL) was disrupted. Horizontal cells formed, and their somata were appropriately aligned, but their neurites did not project laterally. Instead many horizonal cell neurites extended apically, forming ectopic synapses with photoreceptors at all levels of the outer nuclear layer. These ectopic photoreceptor terminals contained synaptic ribbons, horizontal cell processes with synaptic vesicles, and a single mitochrondrion characteristic of rod spherules. Rb‐deficient bipolar cells differentiated normally, extended dendrites to the OPL, and formed synapses that were indistinguishable from adjacent wild‐type cells. In contrast to OPL‐positioned synapses, ectopic synapses did not contain bipolar dendrites. This finding suggests that horizontal cells and photoreceptors can form stable synapses that are devoid of bipolar dendrites outside the normal boundaries of the OPL. Finally, analysis of P4, P7, P12, and P15 retinae suggests that the apical horizontal cell processes result from their failure to establish their normal lateral projections during development. J. Comp. Neurol. 498:112–128, 2006. © 2006 Wiley‐Liss, Inc.
Fast Generalized Distillation for Semi-Supervised Domain Adaptation

Semi-supervised domain adaptation (SDA) is a typical setting when we face the problem of domain adaptation in real applications. How to effectively utilize the unlabeled data is an important issue in SDA. Previous work requires access to the source data to measure the data distribution mismatch, which is ineffective when the size of the source data is relatively large. In this paper, we propose a new paradigm, called Generalized Distillation Semi-supervised Domain Adaptation (GDSDA). We show that without accessing the source data, GDSDA can effectively utilize the unlabeled data to transfer the knowledge from the source models. Then we propose GDSDA-SVM which uses SVM as the base classifier and can efficiently solve the SDA problem. Experimental results show that GDSDA-SVM can effectively utilize the unlabeled data to transfer the knowledge between different domains under the SDA setting.
The neutrophilic and fibrinolytic response to talc can predict the outcome of pleurodesis

It was hypothesised that monitoring neutrophil and d-dimer (DD) levels into the pleural fluid, after talc instillation, could predict the outcome of pleurodesis. The current authors investigated a total of 168 patients with malignant pleural effusion, who were treated with talc poudrage. According to the outcome the patients were categorised into one of two groups, either successful or failed pleurodesis. In all cases, pleural fluid neutrophils and DDs were determined on serial measurements at 0, 3, 24 and 48 h after the procedure. The time course of these parameters was assessed in both groups and the time point at which they could better predict the outcome was further explored. Neutrophils rose rapidly after talc poudrage in both groups, reaching a plateau at 24 h, although in successful pleurodesis this response was significantly higher. DD dropped markedly at 24 h in the group with the successful outcome, but it did not show significant changes in the other group. A cut-off value of 61% for neutrophils and 61 mg·L−1 for the DD at 24 h yielded the best prognosis for successful pleurodesis. The current authors conclude that serial measurements of neutrophil and d-dimer values into the pleural fluid after talc poudrage could be used as predictors of the outcome of pleurodesis.
Semantic Parsing of Pre-university Math Problems

We have been developing an end-to-end math problem solving system that accepts natural language input. The current paper focuses on how we analyze the problem sentences to produce logical forms. We chose a hybrid approach combining a shallow syntactic analyzer and a manually-developed lexicalized grammar. A feature of the grammar is that it is extensively typed on the basis of a formal ontology for pre-university math. These types are helpful in semantic disambiguation inside and across sentences. Experimental results show that the hybrid system produces a well-formed logical form with 88% precision and 56% recall.
Simultaneous analysis of ten low-molecular-mass organic acids in the tricarboxylic acid cycle and photorespiration pathway in Thalassiosira pseudonana at different growth stages.

A method using high-performance liquid chromatography coupled with tandem mass spectrometry was developed for the simultaneous determination of organic acids in microalgae. o-Benzylhydroxylamine was used to derivatize the analytes, and stable isotope-labeled compounds were used as internal standards for precise quantification. The proposed method was evaluated in terms of linearity, recovery, matrix effect, sensitivity, and precision. Linear calibration curves with correlation coefficients >0.99 were obtained over the concentration range of 0.4-40 ng/mL for glycolic acid, 0.1-10 ng/mL for malic acid and oxaloacetic acid, 0.02-2 ng/mL for succinic acid and glyoxylic acid, 4-400 ng/mL for fumaric acid, 20-2000 ng/mL for isocitric acid, 2-200 ng mL-1 for citric acid, 100-10000 ng mL-1 for cis-aconitic acid, and 1-100 ng mL-1 for α-ketoglutaric acid. Analyte recoveries were between 80.2 and 115.1%, and the matrix effect was minimal. Low limits of detection (0.003-1 ng/mL) and limits of quantification (0.01-5 ng/mL) were obtained except cis-aconitic acid. Variations in reproducibility for standard solution at three different concentrations levels were <9%. This is the first report of the simultaneous analysis of ten organic acids in microalgae, which promotes better understanding of their growth state and provides reference value for high-yield microalgae cultures.