Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictive and discriminating three–risk–group prognostic scoring system for staging Hodgkin lymphomas

W e read with interest the article by Maucort–Boulch et al. regarding a new prognostic scoring system for Hodgkin lymphoma. In a series of 955 patients treated between 1981 and 1996, the authors found that only 4 variables present at diagnosis (age, number of lymphoid areas, visceral involvement, and B-symptoms) remained associated with overall survival (OS) on multivariate analysis. The 4 variables were used to identify 6 prognostic groups according to a point system. These groups were then joined to build a 3-stage prognostic scoring system (PSS), the discrimination and prediction properties of which were found to perform better than other prognostic scores tested. We have applied the PSS in a series of 370 patients with Hodgkin lymphoma who were treated with the combination of doxorubicin, bleomycin, vinblastine, and dacarbazine between 1996 and 2005 in 2 public institutions. The median age of the patients was 29 years (range, 15–82 years). There were 197 men (53%) and 173 women. Localized disease, defined as Ann Arbor stages IA-IIA, was present in 151 patients (41%), whereas advanced disease was present in 219 patients. With a median follow–up of 3.92 years in surviving patients, the 5-year OS rate was 87%. The patient distribution across the 6 prognostic groups was: 84 patients in Group 0 (23%), 104 patients in Group 1 (28%), 81 patients in Group 2 (22%), 54 patients in Group 3 (14.5%), 35 patients in Group 4 (9.5%), and 12 patients in Group 5 (3%). The 5year OS rates for these groups were 97%, 93%, 80%, 77%, 86%, and 67%, respectively (P 1⁄4 .0004). The 5-year progression-free survival (PFS) rates of these same groups were 86%, 86%, 74%, 63%, 73%, and 67%, respectively (P 1⁄4 .005). When the PSS was applied, the 5-year OS rates for the early (Groups 0 and 1), intermediate (Groups 2 and 3), and advanced groups (Groups 4 and 5) were 95%, 79%, and 80%, respectively. However, when patients were grouped in a slightly different manner, 3 distinct prognostic groups were clearly identified: early (Groups 0 and 1), with a 5-year OS rate of 95%; intermediate (Groups 2, 3, and 4), with a 5-year OS rate of 81%; and advanced (Group 5), with a 5-year OS rate of 66%. The difference between the early and intermediate groups was significant at a P value of . 0001, but the difference between the intermediate and advanced groups was not found to be significant (P 1⁄4 .1). The same calculation was performed for the 5-year PFS, but we were unable to identify 3 distinct prognostic groups, even when grouping the patients as shown above. We conclude that the PSS did not perform as well in our series as it did in the original study. This finding illustrates anew the difficulties in developing reproducible prognostic systems in the setting of Hodgkin lymphoma.
Primary Self-EXPANDing Nitinol Stenting vs Balloon Angioplasty With Optional Bailout Stenting for the Treatment of Infrapopliteal Artery Disease in Patients With Severe Intermittent Claudication or Critical Limb Ischemia (EXPAND Study)

Purpose: To compare primary placement of a self-expanding nitinol stent to percutaneous transluminal angioplasty (PTA) with bailout stenting in infrapopliteal arteries of patients with severe intermittent claudication or critical limb ischemia (CLI). Methods: In the EXPAND trial (ClinicalTrials.gov; identifier NCT00906022), 92 patients (mean age 72.9±9.5 years; 62 men) undergoing treatment for infrapopliteal stenosis in 11 European centers were randomized 1:1 to either self-expanding nitinol stenting with the Astron Pulsar/Pulsar-18 nitinol stent or PTA with bailout stenting. The primary endpoint was sustainable clinical improvement after 12 months, defined as a ≥1-category increase for Rutherford category 3 patients or a ≥2-category increase for CLI patients (Rutherford categories 4/5) compared with baseline. Furthermore, target lesion revascularization (TLR), mortality, and amputation were assessed after 12 months. Results: Sustained clinical improvement at 1 year was observed in 74.3% of the patients treated with primary stenting and in 68.6% of the patients treated with PTA and bailout stenting (p>0.05). Kaplan-Meier estimates of freedom from TLR (76.6% and 77.6%), mortality (7.4% vs 2.1%), and amputation [8.9% (major 6.7%) vs 13.2% (major 8.7%)] at 1 year were not significantly different. Conclusion: Primary self-expanding nitinol stenting did not show statistically different clinical outcomes compared to angioplasty with bailout stenting for infrapopliteal lesions.
Synaptic and intrinsic mechanisms shape synchronous oscillations in hippocampal neurons in culture

We have detected spontaneous, synchronous calcium oscillations, associated with variations in membrane potential, in hippocampal neurons maintained in primary culture. The oscillatory activity is synaptically driven, as it is blocked by tetrodotoxin, by the glutamate receptor antagonist 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione (CNQX) and by toxins inhibiting neurotransmitter release from presynaptic nerve endings. Neuronal oscillations do not require for their expression the presence of a polyneuronal network and are not primarily influenced by the γ‐aminobutyric acid (GABAA) receptor antagonist picrotoxin, suggesting that they entirely rely on glutamatergic neurotransmission. Synaptic and intrinsic conductances shape the synchronized oscillations in hippocampal neurons. The concomitant activation of N‐methyl‐d‐aspartate (NMDA) receptors and voltage‐activated L‐type calcium channels allows calcium entering from the extracellular medium and sustaining the long depolarization, which shapes every single calcium wave.
Hormonal and Physiological Adaptations to High-Intensity Interval Training in Professional Male Canoe Polo Athletes

Abstract Sheykhlouvand, M, Khalili, E, Agha-Alinejad, H, and Gharaat, M. Hormonal and physiological adaptations to high-intensity interval training in professional male canoe polo athletes. J Strength Cond Res 30(3): 859–866, 2016—This study compared the effects of 2 different high-intensity interval training (HIIT) programs in professional male canoe polo athletes. Responses of peak oxygen uptake (V[Combining Dot Above]O2peak), ventilatory threshold (VT), peak and mean anaerobic power output (PPO and MPO), blood volume, and hormonal adaptations to HIIT were examined. Male athletes (n = 21, age: 24 ± 3 years; height: 181 ± 4 cm; mass: 85 ± 6 kg; and body fat: 12.9 ± 2.7%) were randomly assigned to one of 3 groups (N = 7): (a) (G1) interval paddling with variable volume (6, 7, 8, 9, 9, 9, 8, 7, 6 repetitions per session from first to ninth session, respectively) × 60 second at lowest velocity that elicited V[Combining Dot Above]O2peak (vV[Combining Dot Above]O2peak), 1:3 work to recovery ratio; (b) (G2) interval paddling with variable intensity (6 × 60 second at 100, 110, 120, 130, 130, 130, 120, 110, 100% vV[Combining Dot Above]O2peak from first to ninth session, respectively, 1:3 work to recovery); and (c) (GCON) the control group performed three 60 minutes paddling sessions (75% vV[Combining Dot Above]O2peak) per week for 3 weeks. High-intensity interval training resulted in significant (except as shown) increases compared with pretest, in V[Combining Dot Above]O2peak (G1 = +8.8% and G2 = +8.5%), heart rate at VT (b·min−1) (G1 = +9.7% and G2 = +5.9%) and (%maximum) (G1 = +6.9%; p = 0.29 and G2 = +6.5%), PPO (G1 = +9.7% and G2 = +12.2%), MPO (G1 = +11.1%; p = 0.29 and G2 = +16.2%), total testosterone (G1 = +29.4% and G2 = +16.7%), total testosterone/cortisol ratio (G1 = +40.9% and G2 = +28.1%), and mean corpuscular hemoglobin (G1 = +1.7% and G2 = +1.3%). No significant changes were found in GCON. High-intensity interval paddling may improve both aerobic and anaerobic performances in professional male canoe polo athletes under the conditions of this study.
Role of orbital selectivity on crystal structures and electronic states in BiMnO$_3$ and LaMnO$_3$ perovskites

Correlated oxides, such as BiMnO$_3$ and LaMnO$_3$, show complex interplay of electronic correlations and crystal structure exhibiting multiple first order phase transitions, some without a clear order parameter. The quantitative theoretical description of this temperature dependent electronic-structural interplay in the vicinity of a Mott transition is still a challenge. Here we address this issue by simultaneously considering both structural and electronic degrees of freedom, within a self-consistent density functional theory with embedded dynamical mean field theory. Our results show the existence of novel electronic states characterized by coexistence of insulating, semi-metallic and metallic orbitals. This state is in agreement with resonant X-ray scattering. We also show that electronic entropy plays a decisive role in both electronic and structural phase transitions. By self-consistent determination of both, the electronic state and the corresponding crystal structure, we show that the temperature evolution of these phases can be quantitatively explained from first principles, thus demonstrating the predictive power of the theoretical method for both the structural and the electronic properties.
Measurement of residual breast cancer burden to predict survival after neoadjuvant chemotherapy.

PURPOSE To measure residual disease after neoadjuvant chemotherapy in order to improve the prognostic information that can be obtained from evaluating pathologic response. PATIENTS AND METHODS Pathologic slides and reports were reviewed from 382 patients in two different treatment cohorts: sequential paclitaxel (T) then fluorouracil, doxorubicin, and cyclophosphamide (FAC) in 241 patients; and a single regimen of FAC in 141 patients. Residual cancer burden (RCB) was calculated as a continuous index combining pathologic measurements of primary tumor (size and cellularity) and nodal metastases (number and size) for prediction of distant relapse-free survival (DRFS) in multivariate Cox regression analyses. RESULTS RCB was independently prognostic in a multivariate model that included age, pretreatment clinical stage, hormone receptor status, hormone therapy, and pathologic response (pathologic complete response [pCR] v residual disease [RD]; hazard ratio = 2.50; 95% CI 1.70 to 3.69; P < .001). Minimal RD (RCB-I) in 17% of patients carried the same prognosis as pCR (RCB-0). Extensive RD (RCB-III) in 13% of patients was associated with poor prognosis, regardless of hormone receptor status, adjuvant hormone therapy, or pathologic American Joint Committee on Cancer stage of residual disease. The generalizability of RCB for prognosis of distant relapse was confirmed in the FAC-treated validation cohort. CONCLUSION RCB determined from routine pathologic materials represented the distribution of RD, was a significant predictor of DRFS, and can be used to define categories of near-complete response and chemotherapy resistance.
Pythia: Grammar-Based Fuzzing of REST APIs with Coverage-guided Feedback and Learning-based Mutations

This paper introduces Pythia, the first fuzzer that augments grammar-based fuzzing with coverage-guided feedback and a learning-based mutation strategy for stateful REST API fuzzing. Pythia uses a statistical model to learn common usage patterns of a target REST API from structurally valid seed inputs. It then generates learning-based mutations by injecting a small amount of noise deviating from common usage patterns while still maintaining syntactic validity. Pythia's mutation strategy helps generate grammatically valid test cases and coverage-guided feedback helps prioritize the test cases that are more likely to find bugs. We present experimental evaluation on three production-scale, open-source cloud services showing that Pythia outperforms prior approaches both in code coverage and new bugs found. Using Pythia, we found 29 new bugs which we are in the process of reporting to the respective service owners.
Simulating haplotype blocks in the human genome

SUMMARY A bioinformatic tool was written to simulate haplotypes and SNPs under a modified coalescent with recombination. The most important feature of this program is that it allows for the specification of non-homogeneous recombination rates, which results in the formation of the so-called 'haplotype blocks' of the human genome. The program also implements different mutation models and flexible demographic histories. The samples generated can be very useful to better understand the architecture of the human genome and to investigate its impact in association studies searching for disease genes. AVAILABILITY The SNPsim package is available at http://www.evolgenics. com/software
Discovery of spatio-temporal patterns from location-based social networks

Location-based social networks (LBSNs) such as Twitter or Instagram are a good source for user spatio-temporal behaviour. These networks collect data from users in such a way that they can be seen as a set of collective and distributed sensors of a geographical area. A low rate sampling of user's location information can be obtained during large intervals of time that can be used to discover complex patterns, including mobility profiles, points of interest or unusual events. These patterns can be used as the elements of a knowledge base for different applications in different domains such as mobility route planning, touristic recommendation systems or city planning. The aim of this paper is twofold, first to analyse the frequent spatio-temporal patterns that users share when living and visiting a city. This behaviour is studied by means of frequent itemsets algorithms in order to establish some associations among visits that can be interpreted as interesting routes or spatio-temporal connections. Second, to analyse how the spatio-temporal behaviour of a large number of users can be segmented in different profiles. These behavioural profiles are obtained by means of clustering algorithms that show the different patterns of behaviour of visitors and citizens. The data analysed were obtained from the public data feeds of Twitter and Instagram within an area surrounding the cities of Barcelona and Milan for a period of several months. The analysis of these data shows that these kinds of algorithms can be successfully applied to data from any city (or general area) to discover useful patterns that can be interpreted on terms of singular places and areas and their temporal relationships.
Effectiveness and Safety of 18F-FDG PET in the Evaluation of Dementia: A Review of the Recent Literature

Imaging that can detect pathophysiologic change in the brain holds great promise for diagnostic assessment of patients with Alzheimer disease (AD) and dementia. Although a previous metaanalysis centering on literature from 1990 to 2000 showed a summary accuracy of 86% for 18F-FDG PET for AD diagnosis, the clinical value was considered uncertain because of methodologic shortcomings. Review of the recent literature since 2000 demonstrates that the evidence for 18F-FDG PET in assessment of dementia has increased with new studies that include autopsy confirmation, wide-diagnostic-spectrum recruitment in primary care settings, historical and prospective cohort studies, and multicenter data analyses. These data support the role of 18F-FDG PET as an effective and useful adjunct to other diagnostic information in the assessment of patients with symptoms of dementia. Findings are in line with recently revised diagnostic criteria of AD that for the first time recognize the unique role of biomarker evidence in disease definition.
Hardware Accelerator for Generating Primitive Polynomials over GF(3)

The paper presents a hardware accelerator that could be used to generate irreducible primitive polynomials with coefficients over GF(3). The process of generating a primitive polynomial is done by replicating the other primitive polynomial which is fixed in the device. The implemented algorithm allows the unit to generate all possible primitive polynomials of the same degree as the stored polynomial. This approach allows us to extend the cryptographic power and capabilities of the existing cryptographic devices.
Bridging the information gap between buffer and flash translation layer for flash memory

Flash memory has been widely used as storage media in consumer devices, whereas its erase-before-update characteristic degrades its performance. Buffer and FTL (Flash Translation Layer) are two important techniques to improve the performance of flash memory. However, in the traditional architecture, the buffer and FTL work independently, resulting in an information gap which affects the efficiency of garbage collection in flash memory. This paper proposes a new architecture to bridge the information gap between the buffer and the FTL. In the new architecture, the buffer manager provides several replacement candidates instead of one to the FTL, and the FTL makes and performs a decision according to these candidates and the physical information of flash memory. Experiments show that the new architecture can reduce the garbage collection overhead by up to 40%.
Regulation of the Human High Affinity IgE Receptor β-Chain Gene Expression Via an Intronic Element

The high affinity IgE receptor, FcεRI, is a key regulatory molecule in the allergic reaction. By screening for cis-acting elements over the entire region of the human FcεRI β-chain gene, a sequence located in the fourth intron was revealed to serve as a repressor element. This element was recognized by a transcription factor, myeloid zinc finger protein 1 (MZF-1). Introduction of MZF-1 antisense inhibited the suppressive effect of the element on the β-chain promoter and increased the mRNA for the β-chain in KU812 cells, indicating that MZF-1 repressed human FcεRI β-chain gene expression via the element in the fourth intron. Furthermore, it was suggested that a cofactor binding with MZF-1, whose expression level was different among the cell types, was required for transcriptional repression by MZF-1.
Calumet Ceremonialism as a Nativistic Response

While Hall's (1977) recent paper addressed the origins of calumet symbolism, it did little to explain (or even to acknowledge) the rapid expansion in the usage of the Hako-type calumet and its accompanying ceremony after the opening of the historic period. It is suggested here that this calumet emerged in the role of a stability-enhancing mechanism within precisely those societies that were experiencing rapid sociocultural change and fragmentation. Both the calumet and the tobacco pipe, singly and in combination, constituted cultural elements that had had long identification with the sacred sphere. Not only were calumets and pipes and native tobacco preserved in the new situation, but their conservative ritual significance was greatly emphasized and formalized until they increasingly came to symbolize and embody the old way of life. Archaeological and historical data are used to support this argument.
A Fuzzy Petri Net Model towards Context-Awareness Based Personalized Recommendation

In a personalized recommender system of a ubiquitous computing environment, the decision on recommendation depends on some uncertain factors. Fuzzy system has an ability of solving the reasoning uncertainty, and gets widely used in the context awareness based personalized recommender system. In this paper, we present a fuzzy reasoning model based on the Fuzzy Petri Net. The model considers the requirements of task fulfillment, user's preferences and QoS of the system. With difference from those existing recommender systems, we focus on the formalized modeling of fuzzy reasoning of the personalized recommendation. Through formalization of fuzzy reasoning, we propose an approach to construct a rule-based reasoning system. The feasibility of the proposed approach is validated by an example of the personalized recommender engine.
Frictional Behavior of Individual Vascular Smooth Muscle Cells Assessed By Lateral Force Microscopy

With the advancement of the field of biotribology, considerable interest has arisen in the study of cell and tissue frictional properties. From the perspective of medical device development, the frictional properties between a rigid surface and underlying cells and tissues are of a particular clinical interest. As with many bearing surfaces, it is likely that contact asperities exist at the size scale of single cells and below. Thus, a technique to measure cellular frictional properties directly would be beneficial from both a clinical and a basic science perspective. In the current study, an atomic force microscope (AFM) with a 5 µm diameter borosilicate spherical probe simulating endovascular metallic stent asperities was used to characterize the surface frictional properties of vascular smooth muscle cells (VSMCs) in contact with a metallic endovascular stent. Various treatments were used to alter cell structure, in order to better understand the cellular components and mechanisms responsible for governing frictional properties. The frictional coefficient of the probe on VSMCs was found to be approximately 0.06. This frictional coefficient was significantly affected by cellular crosslinking and cytoskeletal depolymerization agents. These results demonstrate that AFM-based lateral force microscopy is a valuable technique to assess the friction properties of individual single cells on the micro-scale.
Analysis of Ras‐induced oncogenic transformation of NIH‐3T3 cells using differential‐display 2‐DE proteomics

Ras proteins control at least three crucial signalling networks responsible for several cellular processes including anchorage independence, survival, and proliferation. Point mutations in one of the three ras genes are frequent in human tumours. In these tumours, Ras oncoproteins contribute significantly to the malignant phenotype, including deregulation of tumour‐cell growth, apoptosis and invasiveness, and the ability to induce angiogenesis. Although significant strides have been made in understanding Ras biology, the collaborative actions of Ras effectors are still poorly understood. Here, we describe a proteomics approach to study global changes in protein expression in Ras‐transformed NIH3T3 cells. We exploited 2‐D difference gel electrophoresis (DIGE) for pre‐separation fluorescent protein labelling with three separate dyes to reduce gel‐to‐gel variability, to increase sensitivity and dynamic range of protein detection, and to enhance quantification of dysregulated proteins. Proteins dysregulated (> 1.5‐fold) by oncogenic Ras transformation reported to be implicated in Ras‐regulated pathways include S‐methyl‐5‐thioadenosine phosphorylase, stress‐induced‐phosphoprotein 1, galectin‐1, annexin A7 (synexin), 60S acidic ribosomal protein P0, serine/threonine protein phosphatase type 1 (PP1α) and prohibitin. Significantly, we report for the first time the expression of the newly discovered cytokine IL‐25 (or IL‐17E) in mouse embryonic fibroblast cells and its down‐regulation (2.1‐fold) upon Ras‐induced oncogenic transformation.