Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequential Optimization and Shared and Distributed Memory Parallelization in Clusters: N-Body/Particle Simulation

The particle-particle method for N-Body problems is one of the most commonly used methods in computer driven physics simulation. These algorithms are, in general, very simple to design and code, and highly parallelizable. In this article, we present the most important approaches for the application of the three performance improvement areas on these algorithms when executed on high performance computing (HPC) clusters: 1) sequential optimization (a single core in a node of the cluster), 2) shared memory parallelism (in a single node with multiple CPUs available, just like a multiprocessor), and 3) distributed memory parallelism (in the whole cluster). For each one of the improvement areas we present the employed techniques and the obtained performance gain. Also, we will show how some (sequential/classical) code optimizations are almost essential for obtaining at least acceptable parallel performance and scalability.
Clinical course and outcome of essential thrombocythemia and prefibrotic myelofibrosis according to the revised WHO 2016 diagnostic criteria

The recently revised World Health Organization (WHO) classification of myeloid neoplasms recognizes prefibrotic myelofibrosis (prePMF) as a distinct entity, characterized by well-defined histopathologic features together with minor clinical criteria (leukocytes, anemia, increased LDH, splenomegaly). The aim of the study was to examine the clinical relevance of distinguishing prePMF from essential thrombocythemia (ET). We identified in our database all patients affected with ET, prePMF and primary myelofibrosis (PMF) diagnosed according to 2008 WHO criteria with a bone marrow fibrosis grade 0-1 at diagnosis and one DNA sample to define the mutational status. The bone marrow morphology of all 404 identified patients was reviewed by an expert pathologist and patients were reclassified according to the 2016 WHO criteria. After reclassification, our cohort included 269 ET, 109 prePMF, and 26 myeloproliferative neoplasm unclassificable. In comparison with ET, patients with prePMF had higher leukocyte count, lower hemoglobin level, higher platelet count, higher LDH values, and higher number of circulating CD34-positive cells; they showed more frequently splenomegaly (all P values < ·001). CALR mutations were more frequent in prePMF than in ET (35·8% vs 17·8%, P < ·001). PrePMF patients had shorter overall survival (P < ·001) and a trend to a higher incidence of leukemic evolution (P ·067) compared to ET patients, while they did not differ in terms of thrombotic and bleeding complications. In conclusion, ET and prePMF diagnosed according to 2016 WHO criteria are two entities with a different clinical phenotype at diagnosis and a different clinical outcome.
Fetal heart rate variability in growth restricted fetuses

Abstract Intrauterine growth restriction (IUGR) remains a major problem in perinatal medicine because of the variety of its underlying causes and the prediction of its outcome. Characteristics of heartbeat interval patterns are associated with neuro-vegetative and humoral regulatory processes. Fetal magnetocardiography allows non-invasive assessment of these processes with high precision throughout the second half of gestation. The aim of our study was the analysis of linear and non-linear parameters of fetal heart rate fluctuations to distinguish between IUGR fetuses and a cohort of normal subjects, both pre-selected from heart-rate traces representing a quiet state of activity in the third trimester of gestation.
ACHIKO-M Database for high myopia analysis and its evaluation

Myopia is the leading public health concern with high prevalence in developed countries. In this paper, we present the ACHIKO-M fundus image database with both myopic and emmetropic cases for high myopia study. The database contains 705 myopic subjects and 151 normal subjects with both left eye and right eye images for each subject. In addition, various clinical data is also available, allowing correlation study of different risk factors. We evaluated two state-of-the-art automated myopia detection algorithms on this database to show how it can be used. Both methods achieve more than 90% accuracy for myopia diagnosis. We will also discuss how ACHIKO-M can be a good database for both scientific and clinical research of myopia.
Herpes simplex meningo-encephalitis following cochlear implantation: A case study

Abstract Objective and importance Herpes simplex virus (HSV) is reported to be the most common cause of viral encephalitis. Although extremely rare, reactivation of the virus has been reported following central nervous system surgery. To the best of our knowledge, there is no report in the literature that describes HSV encephalitis following cochlear implantation. Clinical presentation We report a case of meningo-encephalitis occurring 17 days after cochlear implantation using an electro-acoustic stimulation device, with oerioperative steroid medication. Intensive anti-viral therapy was given and the patient recovered from the acute illness over 2 weeks. Agitation and anxiety followed the encephalitis and subsequent progress with the cochlear implant was slow. Twelve months after cochlear implantation this patient shows a gradual and steady progress with her hearing rehabilitation. Conclusion Cochlear implantation surgery was either coincidental or was the trigger factor for reactivation of the HSV. Surgeons must be vigilant to post-surgical meningism symptoms particularly if patients have a history of herpes infections.
Does Deep Blue use AI?

When Deep Blue played Garry Kasparov in February 1996 and May 1997, the extensive IBM web pages devoted to the site claimed that Deep Blue did not use artificial intelligence. We argue that this claim is inaccurate, is representative of a wide-spread phenomenon in the field, and is ultimately harmful to AI.
N-Acetylcysteine Prevents Retrograde Motor Neuron Death after Neonatal Peripheral Nerve Injury

Background: Neuronal death may be an overlooked and unaddressed component of disability following neonatal nerve injuries, such as obstetric brachial plexus injury. N-acetylcysteine and acetyl-L-carnitine improve survival of neurons after adult nerve injury, but it is unknown whether they improve survival after neonatal injury, when neurons are most susceptible to retrograde neuronal death. The authors’ objective was to examine whether N-acetylcysteine or acetyl-L-carnitine treatment improves survival of neonatal motor or sensory neurons in a rat model of neonatal nerve injury. Methods: Rat pups received either a sciatic nerve crush or transection injury at postnatal day 3 and were then randomized to receive either intraperitoneal vehicle (5% dextrose), N-acetylcysteine (750 mg/kg), or acetyl-L-carnitine (300 mg/kg) once or twice daily. Four weeks after injury, surviving neurons were retrograde-labeled with 4% Fluoro-Gold. The lumbar spinal cord and L4/L5 dorsal root ganglia were then harvested and sectioned to count surviving motor and sensory neurons. Results: Transection and crush injuries resulted in significant motor and sensory neuron loss, with transection injury resulting in significantly less neuron survival. High-dose N-acetylcysteine (750 mg/kg twice daily) significantly increased motor neuron survival after neonatal sciatic nerve crush and transection injury. Neither N-acetylcysteine nor acetyl-L-carnitine treatment improved sensory neuron survival. Conclusions: Proximal neonatal nerve injuries, such as obstetric brachial plexus injury, produce significant retrograde neuronal death after injury. High-dose N-acetylcysteine significantly increases motor neuron survival, which may improve functional outcomes after obstetrical brachial plexus injury.
Comparison of four methods of estimating glomerular filtration rate in cats.

Four methods of evaluating renal function were performed in 6 cats anesthetized with halothane in oxygen. Glomerular filtration rate (GFR) was measured simultaneously in each cat by exogenous creatinine clearance (ECC), bolus inulin clearance, and 99mTc(Sn)-diethylene-triaminepentaacetic acid (DTPA) clearance determined by 2 different methods. In the first DTPA clearance method (DTPA-1), we measured radioactivity in serial blood specimens to construct plasma disappearance curves for calculation of GFR. In the second DTPA clearance method (DTPA-2), we used serial external head counts of radioactivity and a single blood specimen to construct plasma disappearance curves for calculation of GFR. Bolus inulin clearance was calculated from plasma disappearance curves using a 1-compartment open pharmacokinetic model (IN-1) and a 2-compartment open pharmacokinetic model (IN-2). Glomerular filtration rates were measured over 3 hours, for creatinine and DTPA methods, and over 4 hours for the inulin methods. The GFR obtained with the reference method (ECC) was 2.56 +/- 0.61 ml/min/kg of body weight (mean +/- SD). Values for GFR determined by ECC and DTPA-1 were significantly correlated (r = 0.852; P less than or equal to 0.05). Correlation between ECC and DTPA 2 was not as good (r = 0.783; P less than or equal to 0.10), but the 2 DTPA methods significantly correlated with one another (r = 0.897; P less than or equal to 0.05). (ABSTRACT TRUNCATED AT 250 WORDS)
Decentralized Nonlinear Control Method of Components in Power Systems Based on Differential-Algebrai

Abstract Complete nonlinear differential-algebraic equation (DAE) sub-system models are considered in the paper when designing controllers of components in power systems. First-principle models are nonlinear DAE sub-system models, but they use non-local measurable variables to describe the mutual relation (interconnection) between component and the AC grid, and thus they are not suitable for designing decentralized controllers. In the paper, component structural models are constructed, in which the local-measurable interface variables are used to describe the mutual relation between component and the AC grid. Thus, the proposed models are equivalent to the first-principle models in essence, and have two characteristics: with local measurable interconnections and index 1. These two characteristics make it possible to transform the component structural models to nonlinear ordinary differential equation (ODE) sub-system models with measurable interconnections. Thus, traditional nonlinear control methods which are suitable for nonlinear ODE systems could be developed and expanded to be suitable for designing component controllers.
MALDI-TOF MS in clinical parasitology: applications, constraints and prospects

SUMMARY Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is currently being used for rapid and reproducible identification of bacteria, viruses and fungi in clinical microbiological laboratories. However, some studies have also reported the use of MALDI-TOF MS for identification of parasites, like Leishmania, Giardia, Cryptosporidium, Entamoeba, ticks and fleas. The present review collates all the information available on the use of this technique for parasites, in an effort to assess its applicability and the constraints for identification/diagnosis of parasites and diseases caused by them. Though MALDI-TOF MS-based identification of parasites is currently done by reference laboratories only, in future, this promising technology might surely replace/augment molecular methods in clinical parasitology laboratories.
Application of BRCA1 and BRCA2 mutation carrier prediction models in breast and/or ovarian cancer families of French Canadian descent

The BRCAPRO, Couch, Myriad I and II, Ontario Family History Assessment Tool (FHAT), and Manchester models have been used to predict BRCA1 or BRCA2 mutation carrier status of women at high risk for developing the heritable form of breast and ovarian cancers. We have evaluated these models for their accuracy in classifying 224 French Canadian families with at least three cases of breast cancer (diagnosed before the age of 65 years), ovarian cancer, or male breast cancer where mutation status was known for an index affected case used to assess the model. This series includes 44 BRCA1 and 52 BRCA2 mutation‐positive families. Using receiver operator characteristics analyses, the C‐statistics were found to be 0.81, 0.80, 0.79, and 0.74 for the BRCAPRO, FHAT, Manchester, and Myriad II models, respectively, when incorporating both BRCA1 and BRCA2 mutation carrier predictions. For the BRCAPRO model, 75% scored greater than a 0.43 probability in the mutation‐positive group and 75% scored less than 0.50 in the mutation‐negative group. Only 38 of 128 (30%) mutation‐negative group had a probability greater than 0.43 with the BRCAPRO model. While all models were highly predictive of carrier status, the BRCAPRO model was the most accurate where a cut‐off of 10% would have eliminated 60 of 128 (47%) mutation‐negative families for genetic testing and only miss 10 of 96 (10%) mutation‐positive families. A review of the cancer phenotypes with high BRCAPRO probabilities showed that significantly more metachronous bilateral breast cancer cases occurred in BRCA1/2 mutation carrier families in comparison to mutation‐negative families, a feature which is not discriminated in the BRCAPRO model.
The Role of Strategic and Value Chain Flexibility in Achieving Sustainability Performance: An Empirical Analysis Using Conventional and Consistent PLS

We contribute to the clarification of the link between dynamic and operational capabilities by examining how strategic flexibility and value chain flexibility translate into superior sustainability performance. Using survey data of chemical firms in Germany, our structural equation model shows that value chain flexibility fully mediates the relationship between strategic flexibility and sustainability performance. Further, we contribute to the ongoing research on the partial least squares (PLS) approach to structural equation modeling by estimating the proposed research model with both conventional and consistent PLS (PLSc) and outlining a guideline for evaluating and reporting PLSc-related findings.
Cueing and Logical Problem Solving in Brain Trauma Rehabilitation: Frequency Patterns in Clinician and Patient Behaviors

Frequencies (count per minute) of patient and therapist behaviors during rehabilitation sessions after traumatic brain injury were tracked in order to evaluate an intervention curriculum and the effects of cueing. Frequencies of correct solutions to logical problems and other verbal tasks during speech-language treatments were measured for an adult male with memory impairments and impulsivity who underwent inpatient rehabilitation 14 months after severe traumatic brain injury. Daily frequency of cues by the clinician during the patient’s logic exercises also was measured. These behaviors were recorded each treatment session for 14 weeks. Simple plots of the behavior frequencies were maintained by the clinician on standardized semi-log graph paper. The patient’s performance in solving logical problems improved measurably but gradually. Day-to-day predictability of patient performance was seen, as was predictability in cueing by the clinician. Celerations (trends measured as changes in count per minute per week) in the clinician’s cueing were inversely related to celerations in the patient’s logical problem solving, a pattern evident through multiple reversals. Data from other verbal performance tasks showed no general improvement, nor any pattern of variability paralleling the data on logical problem solving. The data suggest that, for clients with brain trauma, routine continuous measurement of frequencies of behavior may facilitate clinical application of experimental analysis and intervention techniques to improve performance. Measuring the frequency of clinician behavior can help identify the events and conditions that control aspects of patient behavior. Frequency measurement has also been used in physical therapy and occupational therapy, and it is suggested that this method be examined as a common data language for use across rehabilitation disciplines. Copyright © 2000 John Wiley & Sons, Ltd.
Modulation of expression of the hepatitis B virus surface antigen gene by the viral X-gene product

Human hepatoma cells (HepG2 and HUH7) transfected with a plasmid (pHBV1004) containing the transcription units for the major surface antigen (S) mRNA and the X mRNA of hepatitis B virus (HBV) secreted surface antigen (HBsAg) into the culture medium. A frameshift mutation in the X gene carried by pHBV1004 greatly reduced HBsAg production by cells transfected with an equivalent amount of the mutant (pHBV1004-B). The mutation could be complemented by cotransfection with a plasmid (pSV2HBX) containing the X structural gene under control of the SV40 early promoter. HBsAg production by cells cotransfected with pHBV1004-B and pSV2HBX was equivalent to that in cells transfected with the parent plasmid (pHBV1004) alone. Levels of HBsAg production were directly related to the amount of S mRNA produced, showing that the X-gene product (HBxAg) can modulate expression of the S gene.
Differential utilization of the same reading frame in a Xenopus homeobox gene encodes two related proteins sharing the same DNA‐binding specificity.

Xenopus XlHbox 1 produces two transcripts during early development. One encodes a long open reading frame (ORF) and the other a short ORF sharing the same homeodomain, but differing by an 82 amino acid domain at the amino terminus. The long protein amino terminus is conserved with many other homeodomain proteins, and its absence from the short protein could have functional consequences. Some viral genes also utilize a single ORF to encode transcription factors of antagonistic functions. The overall organization of the homologous genes in frog and man is similar, supporting the notion that both transcripts are of functional significance. Studies on XlHbox 1 function show that the region common to the long and short proteins has a sequence‐specific DNA‐binding activity, and that microinjection of specific antibodies into embryos results in the loss of structures derived from cells normally expressing XlHbox 1.
Influence of education and occupation on the incidence of Alzheimer's disease.

OBJECTIVE Several cross-sectional studies have found an association between Alzheimer's disease (AD) and limited educational experience. It has been difficult to establish whether educational experience is a risk factor for AD because educational attainment can influence performance on diagnostic tests. This study was designed to determine whether limited educational level and occupational attainment are risk factors for incident dementia. DESIGN Cohort incidence study. SETTING General community. PARTICIPANTS A total of 593 nondemented individuals aged 60 years or older who were listed in a registry of individuals at risk for dementia in North Manhattan, NY, were identified and followed up. INTERVENTIONS We reexamined subjects 1 to 4 years later with the identical standardized neurological and neuropsychological measures. MAIN OUTCOME MEASURES Incident dementia. RESULTS We used Cox proportional hazards models, adjusting for age and gender, to estimate the relative risk (RR) of incident dementia associated with low educational and occupational attainment. Of the 593 subjects, 106 became demented; all but five of these met research criteria for AD. The risk of dementia was increased in subjects with either low education (RR, 2.02; 95% confidence interval [Cl], 1.33 to 3.06) or low lifetime occupational attainment (RR, 2.25; 95% Cl, 1.32 to 3.84). Risk was greatest for subjects with both low education and low life-time occupational attainment (RR, 2.87; 95% Cl, 1.32 to 3.84). CONCLUSIONS The data suggest that increased educational and occupational attainment may reduce the risk of incident AD, either by decreasing ease of clinical detection of AD or by imparting a reserve that delays the onset of clinical manifestations.
Learning of correlated patterns in spin-glass networks by local learning rules.

Deux prescriptions simples de mise en memoire sont presentees pour les modeles de reseaux imitant le systeme nerveux a N neurones a deux etats. Ces regles sont locales et permettent l'immersion de schemas correles sans erreurs dans un reseau de type verre de spins. A partir d'une configuration arbitraire de liaisons synaptiques, on peut mettre en memoire jusqu'a N schemas par des modifications successives des efficacites synaptiques. On demontre la convergence. Extensions des regles
Unsupervised change detection in built-up areas by multi-temporal polarimetric SAR images

Change detection in large urban areas is an application with increasing relevance. In this domain, Polarimetric SAR (PolSAR) sensors are receiving more attention recently. The enhanced polarimetric information provides useful features which can describe multi-temporal changes. In this work, we aim at introducing an approach for unsupervised change detection with focus on built-up areas that relies on the polarimetric information. This approach is based on the analysis of the multi-temporal α feature obtained from the Cloude-Pottier eigenvalue/eigenvector decomposition. Large differences in the α values can be associated to changes in the dominant scattering mechanism. These are likely to be associated to buildings when built-up areas are considered. Changes are detected according to an automatic and unsupervised approach. Validation is conducted on a pair of UAVSAR images acquired over Los Angeles, USA. Preliminary results highlight the effectiveness of proposed approach.
Unilateral peripheral retinal vascular occlusion in a young Japanese woman with neurofibromatosis-1.

AIEPVM.6 Nevertheless, ICGA demonstrates patchy hyperfluorescence at the level of the RPE as well as multiple small, round, hypofluorescent lesions.6 Furthermore, in the acute phase of MEWDS, there is a decrease in the ERG a-wave amplitude6; our patient showed normal ERGs. Despite the decrease of the EOG ratio observed in one eye of our patient, her familial background for Best disease was negative. This EOG abnormality might reflect the pathologic process located at the level of the RPE. The ocular features and the benign, self-limited clinical course of the disease led the authors to hypothesize that AIEPVM may be an acquired disorder of the RPE, rather than a genetic entity. We also suggest that AIEPVM be included in the differential diagnosis of the white dot syndromes.
Bioprocess enhancement of feather degradation using alkaliphilic microbial mixture

ABSTRACT 1. The main aim of this work is to develop a robust method to generate a microbial mixture which can successfully degrade poultry feathers to overcome environmental problems. 2. Four different alkaliphilic microbes were isolated and shown to degrade poultry feathers. 3. Two of the isolates were phylogenetically identified as Lysinibacillus and the others were identified as Nocardiopsis and Micrococcus. 4. The best microbial co-culture for white and black feather degradation was optimised for pH, temperature and relative population of the isolates to achieve almost 96% of degradation compared with a maximum of 31% when applying each isolate individually. 5. The maximum activity of keratinase was estimated to be 1.5 U/ml after 3 d for white feathers and 0.6 U/ml after 4 d for black feathers in a basal medium containing feather as the main carbon source. Additionally, non-denaturing polyacrylamide gel electrophoresis showed 4 and 3 protease activity bands for white and black feather, respectively. 6. This study provides a robust method to develop potential new mixtures of microorganisms that are able to degrade both white and black feathers by applying a Central Composite Design.