Miracle-dz/UniFAR-FTUs huggingface dataset:
Validity of histology for the diagnosis of paediatric coeliac disease: a Swedish multicentre study

Abstract Objective Histological evaluation of intestinal biopsies for the diagnosis of coeliac disease can be challenging and compatible with risk of misdiagnosis. The aim was to evaluate the agreement of pathological diagnosis for coeliac disease in children investigated at four major paediatric university hospitals in Sweden. Materials and methods Intestinal duodenal biopsies were collected from 402 children at median 9.7 years (1.4–18.3 years). A pathologist at each hospital performed the primary evaluation. A designated pathologist, blinded to the primary evaluation, performed a second Marsh classification of biopsies (M0 to M3c) taken from the bulb and duodenum separately. Kappa (κ) scores between first and second evaluation determined the agreement. Plasma samples were collected at the day of intestinal biopsy and analysed for tissue transglutaminase autoantibodies (tTGA) using radioligand-binding assays. Results Marsh scores were concordant in 229/356 biopsies (64%, κ = 0.52, p < 0.0001). Among discordant results, 15/127 (12%) showed M0 in distal duodenum but ≥ M2 in the bulb, whereas the opposite was true for 8/127 (6%) of the biopsies. There were fewer collected duodenal biopsies, more missing bulb biopsies and missing CD3 staining among discordant evaluations. The second evaluation revealed a Marsh score compliant with coeliac disease in 22 children of whom seven children were tTGA positive. Conclusions The variation between university hospitals on the pathological evaluation of biopsies may lead to misdiagnosis of coeliac disease in paediatric patients. Access to clinical and endoscopic information as well as tTGA levels may be useful for the pathologist to complement the evaluation in dubious cases.
Elucidation of Functional Markers from Aspergillus nidulans Developmental Regulator FlbB and Their Phylogenetic Distribution

Aspergillus nidulans is a filamentous fungus widely used as a model for biotechnological and clinical research. It is also used as a platform for the study of basic eukaryotic developmental processes. Previous studies identified and partially characterized a set of proteins controlling cellular transformations in this ascomycete. Among these proteins, the bZip type transcription factor FlbB is a key regulator of reproduction, stress responses and cell-death. Our aim here was the prediction, through various bioinformatic methods, of key functional residues and motifs within FlbB in order to inform the design of future laboratory experiments and further the understanding of the molecular mechanisms that control fungal development. A dataset of FlbB orthologs and those of its key interaction partner FlbE was assembled from 40 members of the Pezizomycotina. Unique features were identified in each of the three structural domains of FlbB. The N-terminal region encoded a bZip transcription factor domain with a novel histidine-containing DNA binding motif while the dimerization determinants exhibited two distinct profiles that segregated by class. The C-terminal region of FlbB showed high similarity with the AP-1 family of stress response regulators but with variable patterns of conserved cysteines that segregated by class and order. Motif conservation analysis revealed that nine FlbB orthologs belonging to the Eurotiales order contained a motif in the central region that could mediate interaction with FlbE. The key residues and motifs identified here provide a basis for the design of follow-up experimental investigations. Additionally, the presence or absence of these residues and motifs among the FlbB orthologs could help explain the differences in the developmental programs among fungal species as well as define putative complementation groups that could serve to extend known functional characterizations to other species.
Effectiveness of median nerve neural mobilization versus oral ibuprofen treatment in subjects who suffer from cervicobrachial pain: a randomized clinical trial

Introduction Oral ibuprofen (OI) and median nerve neural mobilization (MNNM) are first line treatments for patients who suffer cervicobrachial pain (CP). OI may produce side effects which are not tolerated by all subjects who suffer CP, whereas MNNM has no known side effects. Therefore, the aim of this study was to assess the effectiveness of both treatments (OI vs. MNNM) in CP. Material and methods This investigation was a blinded parallel randomized clinical trial (NCT02593721). Sixty-two participants diagnosed with CP were recruited and randomly assigned to 2 groups (n = 31), which received MNNM or 1200 mg/day OI treatment for 6 weeks. The numeric rating scale for pain intensity was the primary outcome. The cervical rotation range of motion (CROM) and the upper limb function were the secondary outcomes. Results The results showed that OI treatment (η2 = 0.612–0.755) was clearly superior to MNNM (η2 = 0.816–0.821) in all assessments (p < 0.05) except for the CROM device results, which were equivalent to those of the MNNM group (p > 0.05). Three subjects were discharged because of OI side effects. Conclusions Oral ibuprofen may be superior to MNNM for pain reduction and upper limb function increase of subjects with CP. Nevertheless, both treatments were effective. Median nerve neural mobilization may be considered an effective non-pharmaceutical treatment option in subjects with CP. Regarding OI adverse effects, our findings challenge the role of pharmacologic versus manual therapy as possible treatments that may improve pain intensity and upper limb functionality in subjects with CP.
Variability in foraging behaviour of chick-rearing macaroni penguins Eudyptes chrysolophus and its relation to diet

Flexibility in foraging behaviour and diet are characteristics of many penguin species. While these 2 aspects of foraging ecology are presumably tightly coupled, the connection between them is rarely examined directly. Using time-depth recorders and satellite telemetry we documented the foraging behaviour of 43 chick-rearing macaroni penguins Eudyptes chrysolophus at Heard Island. We also compared these behavioural data with prey recovered from the stomach contents of each tracked bird. During guard stage, foraging trips were significantly shorter (average duration = 23 ± 18 h, range = 47 ± 40 km) compared to creche stage (average duration = 115 ± 112 h, range = 169 ± 102 km). Creche stage trips also included significantly more shallow dives that appear to be related to travel (39% of dives <10 m versus 27% for guard stage). Three species dominate the birds' diet: 2 species of euphausiids and the myctophid fish Krefftichthys anderssoni. Over the breeding season, K. anderssoni was taken on trips further from the island with deeper dives compared to the euphausiids. Foraging characteristics also differed between trips targeting different euphausiid prey species; however, there was a temporal shift in the euphausiid species consumed and this was correlated with overall changes in foraging behaviour. Multivariate analysis of behavioural data from trips early in guard stage revealed 2 distinct foraging strategies: deeper and offshore versus shallower and inshore. Individual birds often switched between these strategies in successive trips. The characteristics of many dives performed during inshore trips were indicative of benthic foraging; a previously unrecorded behaviour for macaroni penguins. Euphausiids were captured on both offshore pelagic and inshore benthic trips, illustrating that when prey is found in different habitats substantial changes in foraging parameters can occur independent of dietary shifts. More detailed behavioural studies may allow prey-specific rather than habitat-specific foraging patterns to be distinguished. © Inter-Research 2008.
Effective design strategy for a high-viscosity magnetorheological fluid–based energy absorber with multi-stage radial flow mode

High-viscosity linear polysiloxane–based magnetorheological fluid features its excellent suspension stability. Few reports could be found for magnetorheological energy absorbers using such highly viscous but highly stable magnetorheological fluids as the controlled medium. This study presents a design strategy for the high-viscosity linear polysiloxane–based magnetorheological fluid–based magnetorheological energy absorber with multi-stage radial flow mode. The design strategy is based on the Herschel–Bulkley flow model incorporating minor losses proposed in our prior work. The optimal geometrical parameters were obtained by gradually reducing the number of unknown variables. By analyzing the effect of thicknesses of baffle and outer cylinder and number of coil turns on magnetic circuit, the distribution of magnetic flux in the effective region of magnetorheological valve was optimized. Furthermore, a magnetorheological energy absorber was fabricated and tested using a high-speed drop tower facility with a 600 kg mass. The maximum nominal impact velocity was 4.2 m/s, and the applied current varied discretely from 0, 1, 2, to 3 A. Comparison of our Herschel–Bulkley flow model with measured data was conducted via analysis of peak force, dynamic range, and maximum displacement that indicate the performance of magnetorheological energy absorber. The results validated the effectiveness of the design strategy for the high-viscosity linear polysiloxane–based magnetorheological fluid–based magnetorheological energy absorber.
A New Vegetation Segmentation Approach for Cropped Fields Based on Threshold Detection from Hue Histograms

Over the last decade, the use of unmanned aerial vehicle (UAV) technology has evolved significantly in different applications as it provides a special platform capable of combining the benefits of terrestrial and aerial remote sensing. Therefore, such technology has been established as an important source of data collection for different precision agriculture (PA) applications such as crop health monitoring and weed management. Generally, these PA applications depend on performing a vegetation segmentation process as an initial step, which aims to detect the vegetation objects in collected agriculture fields’ images. The main result of the vegetation segmentation process is a binary image, where vegetations are presented in white color and the remaining objects are presented in black. Such process could easily be performed using different vegetation indexes derived from multispectral imagery. Recently, to expand the use of UAV imagery systems for PA applications, it was important to reduce the cost of such systems through using low-cost RGB cameras Thus, developing vegetation segmentation techniques for RGB images is a challenging problem. The proposed paper introduces a new vegetation segmentation methodology for low-cost UAV RGB images, which depends on using Hue color channel. The proposed methodology follows the assumption that the colors in any agriculture field image can be distributed into vegetation and non-vegetations colors. Therefore, four main steps are developed to detect five different threshold values using the hue histogram of the RGB image, these thresholds are capable to discriminate the dominant color, either vegetation or non-vegetation, within the agriculture field image. The achieved results for implementing the proposed methodology showed its ability to generate accurate and stable vegetation segmentation performance with mean accuracy equal to 87.29% and standard deviation as 12.5%.
Bi - Domain Intraoperative Registration of Vessels

Abstract The segmentation and registration of structures are gaining importance due to the increasing demand of automated image enhancement and understanding. Especially in medicine and life science, assistance systems could have a large impact on diagnosis, treatment and quality control. Dye driven procedures, such as fluorescence imaging with Indocyanine green (ICG), are nowadays indispensable because they enhance contrast, reveal structures and deliver the operator with important information. The contact free ICG angiography is providing the surgeon spatial and temporal information on blood flow within a vessel. The processing of those information is done manually or semi automated but is very helpful for the surgeon. Extending the degree of automatism, the amount of information processed and even augment or transfer it into another domain could deliver the operator useful support and improve surgical work flow. Using, analyzing and transferring those information from ICG-IR domain into the RGB domain is the focus of this project. We are introducing a vessel registration method in the RGB domain driven by the spatial fluorescence behavior of the vessel in the ICG-IR domain. The method includes Superpixel based segmentation of the vessel in the ICG-IR domain, the spatial gradient based transfer and registration in the RGB domain and the continuous segmentation of the vessel in a RGB video. This paper show a proof of concept of the method. The results show an successful inter domain information transfer and registration of the vessel. Further tracking of the vessel over all frames is possible. Nevertheless limitations are revealed and discussed.
A data‐driven approach to modeling power consumption for a hybrid supercomputer

Power consumption of current High Performance Computing systems has to be reduced by at least one order of magnitude before they can be scaled up towards ExaFLOP performance. While we can expect novel hardware technologies and architectures to contribute towards this goal, significant advances have to come also from software technologies such as proactive and power‐aware scheduling, resource allocation, and fault‐tolerant computing. Development of these software technologies in turn relies heavily on our ability to model and accurately predict power consumption in large computing systems. In this paper, we present a data‐driven model of power consumption for a hybrid supercomputer (which held the top spot in the Green500 ranking in June 2013) that combines CPU, GPU, and MIC technologies to achieve high levels of energy efficiency. Our model takes as input workload characteristics—the number and location of resources that are used by each job at a certain time—and calculates a predicted power consumption at the system level. The model is application‐code‐agnostic and is based solely on a data‐driven predictive approach, where log data describing the past jobs in the system are employed to estimate future power consumption. For this, three different model components are developed and integrated. The first employs support vector regression to predict power usage for jobs before these are started. The second uses a simple heuristic to predict the length of jobs, again before they start. The two predictions are then combined to estimate power consumption due to the job at all computational elements in the system. The third component is a linear model that takes as input the power consumption at the computing units and predicts system‐wide power consumption. Our method achieves highly‐accurate predictions starting solely from workload information and user histories. The model can be applied to power‐aware scheduling and power capping: alternative workload dispatching configurations can be evaluated from a power perspective and more efficient ones can be selected. The methodology outlined here can be easily adapted to other HPC systems where the same types of log data are available.
The effect of tibial tuberosity advancement and meniscal release on kinematics of the cranial cruciate ligament-deficient stifle during early, middle, and late stance

Summary Objectives: To evaluate the effect of tibial tuberosity advancement (TTA) and meniscal release on cranial-caudal and axial rotational displacement during early, middle and late stance phases in the canine cranial cruciate ligament- (CCL) deficient stifle. Study design: In vitro biomechanical study. Methods: Eighteen pelvic limbs were evaluated for the effects of TTA on cranial-caudal displacement and axial rotation under a load equivalent to 30% bodyweight, and under the following treatment conditions: normal (intact CCL), CCL deficient, TTA-treated (CCL deficient + TTA), and meniscal release (TTA treated + meniscal release). The limbs were evaluated in the early, middle, and late stance phases using electromagnetic tracking sensors to determine cranial tibial displacement and tibial rotation relative to the femur. Results: Transection of the CCL resulted in significant cranial tibial displacement during early, middle, and late stance (p < 0.0001) and significant internal rotation during early (p = 0.049) and middle stance (p = 0.0006). Performance of TTA successfully eliminated cranial tibial displacement in early, middle, and late stance (p <0.0001) however, the TTA was unsuccessful in normalizing axial rotation in middle stance (p = 0.030). Meniscal release had no effect on cranial-caudal or rotational displacement when performed in conjunction with the TTA. Clinical significance: Tibial tuberosity advancement effectively eliminates cranial tibial displacement during early, middle and late stance however, TTA failed to provide rotational stability in mid-stance.
Cryoanalgesia in Patients Undergoing Nuss Repair of Pectus Excavatum: Technique Modification and Early Results.

PURPOSE The Nuss procedure for surgical correction of pectus excavatum often causes severe postoperative pain. Cryoanalgesia of intercostal nerves is an alternative modality for pain control. We describe our modification of the cryoICE™ probe that allows for nerve ablation through the ipsilateral chest along with early results utilizing this technique. METHODS To allow for ipsilateral nerve ablation, a 20-French chest tube was cut and secured to the cryoICE probe, thus providing insulation for the malleable end of the probe. A 3-year retrospective review of patients undergoing Nuss repair at our institution was performed. Patients who received cryoanalgesia (cryo, n = 6) were compared with a historical control cohort who did not receive cryoanalgesia (nocryo, n = 13) during Nuss repair. Hospital length of stay, postoperative narcotic requirement (PNR), and highest postoperative pain score were collected. RESULTS Both cohorts were similar regarding age, BMI, and pectus index. The cryo group had a significantly less PNR (6.4 versus 17.9 doses, P = .05) and was discharged on average >1 day earlier than nocryo patients (3.7 versus 2.2 days, P = .01). No complications occurred in either group. CONCLUSIONS Our technique modification simplifies previously described approaches to intercostal nerve cryoablation. Patients undergoing this adjunct benefit with less PNR and a faster discharge time.
MassBrowser : Unblocking the Web for the Masses , By the Masses

Existing censorship circumvention systems fail to offer reliable circumvention without sacrificing their users’ QoS, or undertaking high costs of operation. We design a new circumvention system, called MassBrowser, with the objective of addressing such practical weaknesses of existing designs. Our system is based on a new design principle, called “the separation of properties,” that states that circumvention systems should be tailored for circumvention as opposed to offering additional properties like anonymity. We combine various state-of-the-art circumvention techniques to make MassBrowser significantly resistant to blocking, while keeping its cost of operation small ($0.001 per censored client per month). We have built and deployed MassBrowser as a fully operational system with end-user software for regular Internet users. A key part of MassBrowser’s design is using non-censored Internet users to run volunteer proxies to help censored users. We perform the first user study on the willingness of typical Internet users in helping circumvention operators. We have used the findings of our user study in the design of MassBrowser to encourage wide adoption by volunteers; particularly, our GUI software offers high transparency, control, and safety to the volunteers. ∗The first two authors made equal contribution.
Evaluation of p53 protein expression in Barrett esophagus

Background: Loss of heterozygosity of p53 along with aneuploidy is deemed to be the early molecular steps in Barrett metaplasia-dysplasia-adenocarcinoma sequence. Objective biomarkers need to be used along with microscopy for risk stratification to predict the progression of Barrett esophagus (BE) to carcinoma. Aim: This study aims to study p53 protein expression in dysplasia and correlate the same with morphology in BE. Materials and Methods: A time-bound study was conducted from January 2011 to June 2015. All esophageal biopsies showing histological evidence of columnar epithelium with the presence of goblet cells were included. The cases which showed dysplasia were graded on hematoxylin and eosin stain. Evaluation of p53 immunohistochemistry staining was done on all the cases of BE. Dysplasia was correlated with the expression of p53 using Chi-square value (χ2) and Fischer's exact test wherever appropriate. P < 0.05 was considered to be statistically significant. Results: Of 829 esophageal biopsies received, 119 were endoscopically suspected to be BE, of which 85 cases were confirmed on microscopy. In our study, there were 75 cases negative for dysplasia (88.2%), 8 with low-grade dysplasia (LGD) (9.4%), and two with high-grade dysplasia (HGD) (2.4%). Three cases of BE had associated adenocarcinoma. Immunostaining with p53 done on all the 85 cases showed positive staining in all cases with LGD, one with HGD and two with adenocarcinoma. In the present study, immunostaining with p53 showed 90% sensitivity, 89.3% specificity, positive predictive value of 52.9%, and negative predictive value of 98.5%. Conclusion: The technical simplicity, easy availability, and comparatively lower cost enhance the role of p53 as a biomarker in risk stratification for patients with BE.
Transverse momentum dependent (TMD) parton distribution functions: status and prospects

We review transverse momentum dependent (TMD) parton distribution functions, their application to topical issues in high-energy physics phenomenology, and their theoretical connections with QCD resummation, evolution and factorization theorems. We illustrate the use of TMDs via examples of multi-scale problems in hadronic collisions. These include transverse momentum q(T) spectra of Higgs and vector bosons for low q(T), and azimuthal correlations in the production of multiple jets associated with heavy bosons at large jet masses. We discuss computational tools for TMDs, and present the application of a new tool, TMDLIB, to parton density fits and parameterizations.