Miracle-dz/UniFAR-FTUs huggingface dataset:
Hemineglect assessment and rehabilitation using a robotic serious game

Hemineglect is a condition where brain-damaged patients are impaired at perceiving and responding to the contralesional part of objects (allocentric hemineglect) and/or the contralesional part of space (egocentric hemineglect). The condition can also be accompanied by motor impairments. Although treatments exist, none are completely effective. The pipeline objective of our research is to develop a serious game that evaluates and rehabilitates the different forms of hemineglect according to the patient’s impairment severity. The first step towards this objective is the development and validation of a robotic assessment for egocentric hemineglect. We tested 12 stroke patients and 40 healthy control participants with the robotic hemineglect assessment. Patients were also assessed with two hemineglect standardized tests. Significant correlations between the robotic and standardized tests demonstrated a good validity for the assessment of egocentric hemineglect. Moreover, the robotic assessment showed a good sensitivity and specificity. Based on these results, we can identify the captures / components necessary for the serious game rehabilitation to adapt difficulty level in correspondence to the patient’s egocentric hemineglect impairment. Future steps in development will focus on the validation of the allocentric and motor hemineglect assessment. Keywords— hemineglect; spatial attention; assessment; serious game; robot; brain-damage
Dissecting the Role of the S1P/S1PR Axis in Health and Disease

Sphingosine-1-phosphate (S1P) is a pleiotropic sphingophospholipid generated from the phosphorylation of sphingosine by sphingosine kinases (SPHKs). S1P has been experimentally demonstrated to modulate an array of cellular processes such as cell proliferation, cell survival, cell invasion, vascular maturation, and angiogenesis by binding with any of the five known G-protein-coupled sphingosine 1 phosphate receptors (S1P1-5) on the cell surface in an autocrine as well as a paracrine manner. Recent studies have shown that the S1P receptors (S1PRs) and SPHKs are the key targets for modulating the pathophysiological consequences of various debilitating diseases, such as cancer, sepsis, rheumatoid arthritis, ulcerative colitis, and other related illnesses. In this article, we recapitulate these novel discoveries relative to the S1P/S1PR axis, necessary for the proper maintenance of health, as well as the induction of tumorigenic, angiogenic, and inflammatory stimuli that are vital for the development of various diseases, and the novel therapeutic tools to modulate these responses in oral biology and medicine.
Native valve Aspergillus endocarditis in two patients with aplastic anaemia

Native valve fungal endocarditis is an uncommon disease with a high mortality rate. We present the clinical features, histological findings and outcome of 2 patients with native valve Aspergillus endocarditis. Both patients had aplastic anaemia as a predisposing disease. The diagnosis was made by Duke's criteria in 1 case and by histology in the other. Surgery was precluded owing to profound thrombocytopenia. Both patients had fatal outcome despite administration of liposomal amphotericin β.
Prevalence of Overweight and Obesity among Chinese Adults: Role of Adiposity Indicators and Age

Objectives: The role of different body fat indicators and age in assessing the prevalence of obesity is unclear. We aimed to examine to what extent different body fat indicators including BMI, waist circumference (WC) and waist-to-hip ratio (WHR) affect the prevalence of overweight and obesity among Chinese adults taking age into account. Methods: This population-based cross-sectional study included a random sample of 7,603 adults aged 20-79 years across entire Tianjin, China. BMI, WC, and WHR were used to define overweight and obesity following standard criteria. Prevalence rates were calculated and standardized using local age- and gender-specific census data. Logistic regression was used in data analysis. Results: Using the combination of BMI, WC, and WHR, the prevalence of overweight and obesity was 69.8%, and increased with age till the age of 60 and a decline thereafter. The prevalence of overweight assessed by BMI was higher than that assessed by WC and WHR, while the prevalence of obesity defined by BMI was much lower than that defined by WC or WHR. Conclusion: The prevalence of overweight and obesity is about 70% among Chinese adults. Adiposity indicators and age play an important role in the prevalence of overweight and obesity.
Nitrate Enhances the Survival of Mycobacterium tuberculosis during Inhibition of Respiration

ABSTRACT When oxygen is slowly depleted from growing cultures of Mycobacterium tuberculosis, they enter a state of nonreplicating persistence that resembles the dormant state seen with latent tuberculosis. In this hypoxic state, nitrate reductase activity is strongly induced. Nitrate in the medium had no effect on long-term persistence during gradual oxygen depletion (Wayne model) for up to 46 days, but significantly enhanced survival during sudden anaerobiosis. This enhancement required a functional nitrate reductase. Thioridazine is a member of the class of phenothiazines that act, in part, by inhibiting respiration. Thioridazine was toxic to both actively growing and nonreplicating cultures of M. tuberculosis. At a sublethal concentration of thioridazine, nitrate in the medium improved the growth. At lethal concentrations of thioridazine, nitrate increased survival during aerobic incubation as well as in microaerobic cultures that had just entered nonreplicating persistence (NRP-1). In contrast, the survival of anaerobic persistent (NRP-2) cultures exposed to thioridazine was not increased by the addition of nitrate. Nitrate reduction is proposed to play a role during the sudden interruption of aerobic respiration due to causes such as hypoxia, thioridazine, or nitric oxide.
Congenital limb deficiencies in Alberta—a review of 33 years (1980–2012) from the Alberta Congenital Anomalies Surveillance System (ACASS)

The birth prevalence of limb deficiencies in Alberta has been fluctuating. The objectives were to examine patterns and temporal trends of congenital limb deficiencies in Alberta and compare rates with those of other jurisdictions. The Alberta Congenital Anomalies Surveillance System data on live births, stillbirths, and terminations of pregnancy (<20 weeks gestation) occurring between 1980 through 2012 with the ICD‐10 Royal College of Paediatrics and Child Health Adaptations codes Q71‐Q73 (limb reduction defects), Q79.80 (congenital constriction bands), and Q87.24 (sirenomelia syndrome) were reviewed. Cases were classified as having amelia, transverse, longitudinal (preaxial, postaxial, central, or mixed), intercalary, split hand/split foot, complex, or other type of limb deficiency. Phenotypes were classified as associated, which included cases with a known etiology and cases with at least one other type of anomaly, or isolated. From 1980 through 2012, 795 cases were ascertained from 1,411,652 live births and stillbirths, giving a prevalence of 5.6/10,000 total births. Mixed longitudinal deficiencies were the most common (22.4%). The upper limbs (63.9%) were affected more often than the lower limbs (25.3%). Isolated limb deficiencies occurred in 43.6% of cases, 28.4% had Mendelian or other known conditions, 21.9% had multiple congenital anomalies, 5.4% had chromosome abnormalities and 0.6% were due to teratogens. The associated group, showed a significant increasing trend (P = 0.023). While the overall limb deficiency rates show very little differences across diverse populations and differing time periods, comparisons of subgroups should be made with caution, because variations in terminology and classification contribute to reported differences. © 2015 Wiley Periodicals, Inc.
Assimetria na Volatilidade de Commodities Agrícola

Este estudo tem por objetivo analisar o comportamento temporal das taxas de retorno e da volatilidade de cinco commodities agricola no mercado brasileiro. Para o desenvolvimento deste estudo, foram considerados os indices mensais de preco medio recebidos pelo produtor em moeda corrente deflacionados pelo IGP-DI/FGV. O conjunto de dados abrange o periodo de janeiro de 1967 a fevereiro de 2006 e foram obtidos do banco de dados da FGV. As commodities analisadas foram: Algodao em caroco, Cafe em coco, Milho, Soja e Trigo. Com base nos resultados obtidos, pode-se afirmar que para todas as commodities analisadas, ocorre o efeito de dependencia positiva relacionado ao periodo imediatamente anterior. Identificou se que a serie retornos do Milho e a que mais sofre influencia de eventos passados. Para a volatilidade, identificou-se o efeito alavancagem apenas para o Trigo.
Loss of Function but No Gain of Function Caused by Amino Acid Substitutions in the Hexapeptide of Hoxa1 In Vivo

ABSTRACT Homeodomain containing transcription factors of the Hox family play critical roles in patterning the anteroposterior embryonic body axis, as well as in controlling several steps of organogenesis. Several Hox proteins have been shown to cooperate with members of the Pbx family for the recognition and activation of identified target enhancers. Hox proteins contact Pbx via a conserved hexapeptide motif. Previous biochemical studies provided evidence that critical amino acid substitutions in the hexapeptide sequence of Hoxa1 abolish its interaction with Pbx. As a result, these substitutions also abolish Hoxa1 activity on known target enhancers in cellular models, suggesting that Hoxa1 activity relies on its capacity to interact with Pbx. Here, we show that mice with mutations in the Hoxa1 hexapeptide display hindbrain, cranial nerve, and skeletal defects highly reminiscent of those reported for the Hoxa1 loss of function. Since similar hexapeptide mutations in the mouse Hoxb8 and the Drosophila AbdA proteins result in activity modulation and gain of function, our data demonstrate that the functional importance of the hexapeptide in vivo differs according to the Hox proteins.
Is the absolute value of O(6)-methylguanine-DNA methyltransferase gene messenger RNA a prognostic factor, and does it predict the results of treatment of glioblastoma with temozolomide?

OBJECTIVES Methylation of O(6)-methylguanine-DNA methyltransferase (MGMT) has been reported to be a good prognostic factor for patients with glioblastoma multiforme (GBM). To determine whether the absolute value of MGMT messenger RNA (mRNA) might be a prognostic factor and useful for predicting the therapeutic effectiveness of temozolomide, especially with regard to GBMs, the authors measured the absolute value of MGMT mRNA in gliomas by using real-time reverse-transcription polymerase chain reaction (RT-PCR). METHODS MGMT mRNA was measured in 140 newly diagnosed gliomas by real-time RT-PCR using the Taq-Man probe. Among 73 GBMs, 45 had been initially treated with temozolomide and radiation. RESULTS The mean MGMT mRNA value was significantly lower in oligodendroglial tumors than in other tumors. In the 73 GBMs, a significant prognostic factor for progression-free survival was fewer than 1000 copies/ μgRNA of MGMT mRNA (p = 0.0150). Of 45 patients with GBMs that had been treated with temozolomide and radiation, progression-free survival was significantly longer for those whose GMB had fewer than 1000 copies/μgRNA of MGMT mRNA than for those whose GBM had more than 1000 copies/μgRNA (p = 0.0090). In 32 patients with GBMs treated by temozolomide and radiation whose age was younger than 75 years and whose Karnofsky Performance Scale score was more than 70, progression-free and overall survival times were longer for those with GBMs of fewer than 5000 copies/μgRNA of MGMT mRNA than for those with GBMs of more than 5000 copies/μgRNA (p = 0.0365 and p = 0.0312). CONCLUSIONS MGMT mRNA might be useful as a prognostic factor and for predicting the results of therapy for GBMs treated by temozolomide. New individual adjuvant therapy based on the results of MGMT mRNA quantitation has been proposed.
EVector: An efficient vector implementation - Using virtual memory for improving memory

Every modern operating system provides some form of virtual memory to its applications. Usually, a hardware memory management unit (MMU) exists to efficiently support this. Although most operating systems allow user programs to indirectly control the MMU, few programs or programming languages actually make use of this facility. This article explores how the MMU can be used to enhance memory handling for resizable arrays. A reference implementation in C++ demonstrates its usability and superiority compared to the standard C++ vector class, and how to combine the scheme with an object-oriented environment. A number of other improvements, based on newly emerged insights in C++ are also presented.
Control of flexible manipulators: A survey

A survey of the field of control for flexible multi-link robots is presented. This research area has drawn great attention during the last two decades, and seems to be somewhat less “attractive” now, due to the many satisfactory results already obtained, but also because of the complex nature of the remaining open problems. Thus it seems that the time has come to try to deliver a sort of “state of the art” on this subject, although an exhaustive one is out of scope here, because of the great amount of publications. Instead, we survey the most salient progresses – in our opinion – approximately during the last decade, that are representative of the essential different ideas in the field. We proceed along with the exposition of material coming from about 119 included references. We do not pretend to deeply present each of the methods quoted hereafter; however, our goal is to briefly introduce most of the existing methods and to refer the interested reader to more detailed presentations for each scheme. To begin with, a now well-established classification of the flexible arms control goals is given. It is followed by a presentation of different control strategies, indicating in each case whether the approach deals with the one-link case, which can be successfully treated via linear models, or with the multi-link case which necessitates nonlinear, more complex, models. Some possible issues for future research are given in conclusion.
Learning tubes

We present a new method for analyzing data manifolds based on Weyls tube theorem. The coefficients of the tube polynomial for a manifold provide geometric information such as the volume of the manifold or its Euler characteristic, thus providing bounds on the geometric nature of the manifold. We present an algorithm estimating the coefficients of the tube polynomial for a given manifold and demonstrate the features of our algorithm on artificial data sets. We apply the algorithm on a real-world traffic data set to determine the number and properties of clusters. We furthermore demonstrate that our algorithm can be used to determine image coverage of an object, giving hints on where a manifold is not sufficiently sampled.
The plastocyanin binding domain of photosystem I.

The molecular recognition between plastocyanin and photosystem I was studied. Photosystem I and plastocyanin can be cross‐linked to an active electron transfer complex. Immunoblots and mass spectrometric analysis of proteolytic peptides indicate that the two negative patches conserved in plant plastocyanins are cross‐linked with lysine residues of a domain near the N‐terminus of the PsaF subunit of photosystem I. Conversion of these negative to uncharged patches of plastocyanin by site‐directed mutation D42N/E43Q/D44N/E45Q and E59Q/E60Q/D61N respectively, reveals the first patch to be essential for the electrostatic interaction in the electron transfer complex with photosystem I and the second one to lower the redox potential. The domain in PsaF, not found in cyanobacteria, is predicted to fold into two amphipathic alpha‐helices. The interacting N‐terminal helix lines up six lysines on one side which may guide a fast one‐dimensional diffusion of plastocyanin and provide the electrostatic attraction at the attachment site, in addition to the hydrophobic interaction in the area where the electron is transferred to P700 in the reaction center of photosystem I. This two‐step interaction is likely to increase the electron transfer rate by more than two orders of magnitude in plants as compared with cyanobacteria. Our data resolve the controversy about the function of PsaF.
CHAPTER 89 Esophagus , Stomach , and Duodenum

Patients with ingestion of foreign objects and esophageal food boluses commonly are seen in the emergency department (ED). Although most objects pass spontaneously, approximately 10 to 20% require a nonoperative intervention, and fewer than 1% require surgical removal. Death as a result of foreign body ingestion or impaction is rare. Patients with esophageal foreign bodies can be classified into four major categories: (1) pediatric patients, (2) psychiatric patients and prisoners, (3) patients with underlying esophageal disease, and (4) edentulous adults. Pediatric patients account for more than 75% of ingestions, with the peak incidence between the ages of 18 and 48 months. Coins account for the majority of pediatric ingestions, whereas most adult impactions involve pieces of food, particularly meat and bones. Patients with structural abnormalities of the esophagus, such as strictures, rings, webs, diverticuli, or malignancies, are at greater risk for foreign body impaction. Edentulous adults are also at increased risk because of impaired oral sensation and have a risk of accidental ingestion of their dental prosthesis.
A new item-based deep network structure using a restricted Boltzmann machine for collaborative filtering

The collaborative filtering (CF) technique has been widely used recently in recommendation systems. It needs historical data to give predictions. However, the data sparsity problem still exists. We propose a new item-based restricted Boltzmann machine (RBM) approach for CF and use the deep multilayer RBM network structure, which alleviates the data sparsity problem and has excellent ability to extract features. Each item is treated as a single RBM, and different items share the same weights and biases. The parameters are learned layer by layer in the deep network. The batch gradient descent algorithm with minibatch is used to increase the convergence speed. The new feature vector discovered by the multilayer RBM network structure is very effective in predicting a rating and achieves a better result. Experimental results on the data set of MovieLens show that the item-based multilayer RBM approach achieves the best performance, with a mean absolute error of 0.6424 and a root-mean-square error of 0.7843.
Monte Carlo patient study on the comparison of prompt gamma and PET imaging for range verification in proton therapy

The purpose of this work was to compare the clinical adaptation of prompt gamma (PG) imaging and positron emission tomography (PET) as independent tools for non-invasive proton beam range verification and treatment validation. The PG range correlation and its differences with PET have been modeled for the first time in a highly heterogeneous tissue environment, using different field sizes and configurations. Four patients with different tumor locations (head and neck, prostate, spine and abdomen) were chosen to compare the site-specific behaviors of the PG and PET images, using both passive scattered and pencil beam fields. Accurate reconstruction of dose, PG and PET distributions was achieved by using the planning computed tomography (CT) image in a validated GEANT4-based Monte Carlo code capable of modeling the treatment nozzle and patient anatomy in detail. The physical and biological washout phenomenon and decay half-lives for PET activity for the most abundant isotopes such as 11C, 15O, 13N, 30P and 38K were taken into account in the data analysis. The attenuation of the gamma signal after traversing the patient geometry and respective detection efficiencies were estimated for both methods to ensure proper comparison. The projected dose, PG and PET profiles along many lines in the beam direction were analyzed to investigate the correlation consistency across the beam width. For all subjects, the PG method showed on average approximately 10 times higher gamma production rates than the PET method before, and 60 to 80 times higher production after including the washout correction and acquisition time delay. This rate strongly depended on tissue density and elemental composition. For broad passive scattered fields, it was demonstrated that large differences exist between PG and PET signal falloff positions and the correlation with the dose distribution for different lines in the beam direction. These variations also depended on the treatment site and the particular subject. Thus, similar to PET, direct range verification with PG in passive scattering is not easily viable. However, upon development of an optimized 3D PG detector, indirect range verification by comparing measured and simulated PG distributions (currently being explored for the PET method) would be more beneficial because it can avoid the inherent biological challenges of the PET imaging. The improved correlation of PG and PET with dose when using pencil beams was evident. PG imaging was found to be potentially advantageous especially for small tumors in the presence of high tissue heterogeneities. Including the effects of detector acceptance and efficiency may hold PET superior in terms of the amplitude of the detected signal (depending on the future development of PG detection technology), but the ability to perform online measurements and avoid signal disintegration (due to washout) with PG are important factors that can outweigh the benefits of higher detection sensitivity.
Climate regulation of fire emissions and deforestation in equatorial Asia

Drainage of peatlands and deforestation have led to large-scale fires in equatorial Asia, affecting regional air quality and global concentrations of greenhouse gases. Here we used several sources of satellite data with biogeochemical and atmospheric modeling to better understand and constrain fire emissions from Indonesia, Malaysia, and Papua New Guinea during 2000–2006. We found that average fire emissions from this region [128 ± 51 (1σ) Tg carbon (C) year−1, T = 1012] were comparable to fossil fuel emissions. In Borneo, carbon emissions from fires were highly variable, fluxes during the moderate 2006 El Niño more than 30 times greater than those during the 2000 La Niña (and with a 2000–2006 mean of 74 ± 33 Tg C yr−1). Higher rates of forest loss and larger areas of peatland becoming vulnerable to fire in drought years caused a strong nonlinear relation between drought and fire emissions in southern Borneo. Fire emissions from Sumatra showed a positive linear trend, increasing at a rate of 8 Tg C year−2 (approximately doubling during 2000–2006). These results highlight the importance of including deforestation in future climate agreements. They also imply that land manager responses to expected shifts in tropical precipitation may critically determine the strength of climate–carbon cycle feedbacks during the 21st century.