Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct Innate Immunity Pathways to Activation and Tolerance in Subgroups of Chronic Lymphocytic Leukemia with Distinct Immunoglobulin Receptors

Subgroups of patients with chronic lymphocytic leukemia (CLL) have distinct expression profiles of Toll-like receptor (TLR) pathway-associated genes. To test the hypothesis that signaling through innate immunity receptors may influence the behavior of the malignant clone, we investigated the functional response triggered by the stimulation of TLRs and NOD2 in 67 CLL cases assigned to different subgroups on the basis of immunoglobulin heavy variable (IGHV) gene usage, IGHV gene mutational status or B-cell receptor (BcR) stereotypy. Differences in the induction of costimulatory molecules and/or apoptosis were observed in mutated versus unmutated CLL. Different responses were also identified in subsets with stereotyped BcRs, underscoring the idea that “subset-biased” innate immunity responses may occur independently of mutational status. Additionally, differential modulation of kinase activities was induced by TLR stimulation of different CLL subgroups, revealing a TLR7-tolerant state for cases belonging to stereotyped subset #4. The distinct patterns of TLR/NOD2 functional activity in cells from CLL subgroups defined by the molecular features of the clonotypic BcRs might prove relevant for elucidating the immune mechanisms underlying CLL natural history and for defining subgroups of patients who might benefit from treatment with specific TLR ligands.
Fractional order sliding mode control for attitude and altitude stabilization of a quadrotor UAV

This paper presents a novel fractional order sliding mode control strategy for a quadrotor unmanned aerial vehicle attitude and altitude stabilization. A saturated dynamic model is first obtained via Euler-Lagrange mechanics and coordinate translation. By introducing fractional order calculus, the newly presented control law can achieve fast convergence speed. In addition, with the help of bounded functions, our controller can deal with input limitation caused by characteristics of motors and propellers. Finally, simulations are carried out to illustrate the effectiveness of our method.
Impact of rapid diagnosis on management of adults hospitalized with influenza.

BACKGROUND Rapid influenza testing decreases antibiotic and ancillary test use in febrile children, yet its effect on the care of hospitalized adults is unexplored. We compared the clinical management of patients with influenza whose rapid antigen test result was positive (Ag+) with the management of those whose rapid antigen test result was negative or the test was not performed (Ag0). METHODS Medical record review was performed on patients with influenza hospitalized during 4 winters (1999-2003). Hospital policy mandated influenza testing (antigen or culture) for all patients with acute cardiopulmonary diseases admitted from November 15 through April 15. A subset of patients participated in an epidemiological study and had reverse-transcriptase polymerase chain reaction or serologic testing performed. Clinical data from Ag+ and Ag0 patients were compared. RESULTS Of 166 patients with available records, 86 were Ag+ and 80 were Ag0. Antibiotic use (74 [86%] of 86 patients vs 79 [99%] of 80 patients; P = .002) was less and antibiotic discontinuance (12 [14%] of 86 patients vs 2 [2%] of 80 patients; P=.01) was greater in Ag+ compared with Ag0 patients. No significant differences in antibiotic days, length of hospital stay, or antibiotic complications were noted. Antiviral use (63 [73%] of 86 patients vs 6 [8%] of 80 patients; P<.001) was greater in Ag+ than Ag0 patients. Antigen status was independently associated with withholding or discontinuing antibiotics in multivariate analysis. Of 44 Ag+ patients deemed low risk for bacterial infection, 27 continued to receive antibiotics despite positive influenza test results. These patients more commonly had pulmonary disease and had significantly more abnormal lung examination results (P = .005) compared with those in whom antibiotics were withheld or discontinued. CONCLUSIONS Rapid influenza testing leads to reductions in antibiotic use in hospitalized adults. Better tools to rule out concomitant bacterial infection are needed to optimize the impact of viral testing.
A wavelet based analysis of energy redistribution in scalp EEG during epileptic seizures

In this work, wavelet decomposition and multiresolution analysis are used to explore the changes in scalp EEG signals during epileptic seizures. EEG tracings, which include non-epileptic periods, the beginning of seizure and the peak of seizure, have been decomposed in five details using order 10 Daubechies orthonormal wavelets. Energy has then been computed, at each detail, from square wavelet coefficients, in order to unmask the presence of brief episodes of energy relocation among different scales. Results reveal the existence of significant changes in energy distribution at seizure onset; this redistribution, however, exhibits significant differences from one patient to another, and also among different channels in the same patient. Some channels exhibit a significant energy increase at low scales (high frequencies greater than 20 Hz) at seizure onset, whereas energy drops at higher scales. Other channels, however, exhibit energy increase at high scales (frequency less than 15 Hz) revealing a predominance of low-frequency activity. These two patterns may be simultaneously present at seizure onset and may change with different spatial evolution during the subsequent seizure progression. Wavelet analysis appears as a powerful tool for extracting features relative to seizure, and to study their propagation among different regions in the scalp.
Final version of 2009 AJCC melanoma staging and classification.

PURPOSE To revise the staging system for cutaneous melanoma on the basis of data from an expanded American Joint Committee on Cancer (AJCC) Melanoma Staging Database. METHODS The melanoma staging recommendations were made on the basis of a multivariate analysis of 30,946 patients with stages I, II, and III melanoma and 7,972 patients with stage IV melanoma to revise and clarify TNM classifications and stage grouping criteria. RESULTS Findings and new definitions include the following: (1) in patients with localized melanoma, tumor thickness, mitotic rate (histologically defined as mitoses/mm(2)), and ulceration were the most dominant prognostic factors. (2) Mitotic rate replaces level of invasion as a primary criterion for defining T1b melanomas. (3) Among the 3,307 patients with regional metastases, components that defined the N category were the number of metastatic nodes, tumor burden, and ulceration of the primary melanoma. (4) For staging purposes, all patients with microscopic nodal metastases, regardless of extent of tumor burden, are classified as stage III. Micrometastases detected by immunohistochemistry are specifically included. (5) On the basis of a multivariate analysis of patients with distant metastases, the two dominant components in defining the M category continue to be the site of distant metastases (nonvisceral v lung v all other visceral metastatic sites) and an elevated serum lactate dehydrogenase level. CONCLUSION Using an evidence-based approach, revisions to the AJCC melanoma staging system have been made that reflect our improved understanding of this disease. These revisions will be formally incorporated into the seventh edition (2009) of the AJCC Cancer Staging Manual and implemented by early 2010.
Alpha-Particle-Induced Soft Error Rate in VLSI Circuits

We study soft error rates (SER) in VLSI circuits, where the charge capable of causing a soft error becomes only a few percent of that created by a typical alpha-particle impacting on the circuits. Theoretical investigations are done considering a DRAM test vehicle, with the assumption that it is exposed to alpha-particles emanating from materials on the chip. We examine the effects of scaling on the SER and investigate the performance of several device structural modifications that can be introduced to decrease SER. We present experimental results on the achieved reduction in the charge that surface nodes collect when structural modifications are introduced. We find, both experimentally and theoretically, that the most promising modification is the incorporation of a buried grid of opposite conductivity type from the substrate. In general, however, as stored change shrinks, multiple errors become prevalent, and SER reduction due to fabrication changes becomes less effective.
Does Rule of Law Affect Economic Growth Positively

Efficient institutional structure resolves the uncertainties in the market and the problem of asymmetric information, and thus creates a positive exogeneity, ensures the efficient distribution of the resources and makes a positive impact on the functioning of the economy. In addition to this, especially rule of law forms the basis of the socio-economic development. In the presence of the factors such as prevention of corruption and freedom of expression, institutional structure has a significant impact on economic growth. However, there are empirical studies that state that institutional efficiency boosts economic growth in developed countries, whereas it doesn’t have an impact or has a negative impact on economic growth in developing countries. For all these reasons, the impact of institutional efficiency on economic growth in developed, developing and underdeveloped countries will be analyzed in this study. In this study, the effect of institutional effectiveness on economic growth has been analyzed in both three country groups from 2002 to 2015 by using GMM. Dependent variable is GDP and the independent variables are institutional variables (rule of law, fight against corruption, voice and accountability). Based on our primitive findings we expect that developed institutions effect economic growth positively in develop countries unlike developing countries.
Swarming Differentiation and Swimming Motility in Bacillus subtilis Are Controlled by swrA, a Newly Identified Dicistronic Operon

ABSTRACT The number and disposition of flagella harbored by eubacteria are regulated by a specific trait successfully maintained over generations. The genes governing the number of flagella in Bacillus subtilis have never been identified, although the ifm locus has long been recognized to influence the motility phenotype of this microorganism. The characterization of a spontaneous ifm mutant of B. subtilis, displaying diverse degrees of cell flagellation in both liquid and solid media, raised the question of how the ifm locus governs the number and assembly of functional flagella. The major finding of this investigation is the characterization of a newly identified dicistronic operon, named swrA, that controls both swimming motility and swarming differentiation in B. subtilis. Functional analysis of the swrA operon allowed swrAA (previously named swrA [D. B. Kearns, F. Chu, R. Rudner, and R. Losick, Mol. Microbiol. 52:357-369, 2004]) to be the first gene identified in B. subtilis that controls the number of flagella in liquid environments and the assembly of flagella in response to cell contact with solid surfaces. Evidence is given that the second gene of the operon, swrAB, is essential for enabling the surface-adhering cells to undergo swarming differentiation. Preliminary data point to a molecular interaction between the two gene products.
Comparative Safety of Testosterone Dosage Forms.

IMPORTANCE Increases in testosterone use and mixed reports of adverse events have raised concerns about the cardiovascular safety of testosterone. Testosterone is available in several delivery mechanisms with varying pharmacokinetics; injections cause spikes in testosterone levels, and transdermal patches and gels cause more subtle but sustained increases. The comparative cardiovascular safety of gels, injections, and patches has not been studied. OBJECTIVE To determine the comparative cardiovascular safety of testosterone injections, patches, and gels. DESIGN, SETTING, AND PARTICIPANTS A retrospective cohort study was conducted using administrative claims from a commercially insured (January 1, 2000, to December 31, 2012) and Medicare (January 1, 2007, to December 31, 2010) population in the United States and general practitioner records from the United Kingdom (January 1, 2000, to June 30, 2012). Participants included men (aged ≥18 years) who initiated use of testosterone patches, gels, or injections following 180 days with no testosterone use. Our analysis was conducted from December 11, 2013, to November 12, 2014. EXPOSURES New initiation of a testosterone dosage form, with use monitored for up to 1 year. MAIN OUTCOMES AND MEASURES Inpatient or outpatient medical records, diagnoses, or claims for cardiovascular and cerebrovascular events including myocardial infarction (MI), unstable angina, stroke, and composite acute event (MI, unstable angina, or stroke); venous thromboembolism (VTE); mortality; and all-cause hospitalization. RESULTS We identified 544,115 testosterone initiators between the 3 data sets: 37.4% injection, 6.9% patch, and 55.8% gel. The majority of men in the Medicare cohort were injection initiators (51.2%), most in the US commercially insured population were gel initiators (56.5%), and the UK database included equal proportions of injections and gel users (approximately 41%). With analysis conducted using hazard ratios and 95% CIs, compared with men using gels, injection initiators had higher hazards of cardiovascular events (ie, MI, unstable angina, and stroke) (1.26; 1.18-1.35), hospitalization (1.16; 1.13-1.19), and death (1.34; 1.15-1.56) but not VTE (0.92; 0.76-1.11). Compared with gels, patches did not confer increased hazards of cardiovascular events (1.10; 0.94-1.29), hospitalization (1.04; 1.00-1.08), death (1.02; 0.77-1.33), or VTE (1.08; 0.79-1.47). CONCLUSIONS AND RELEVANCE Testosterone injections were associated with a greater risk of cardiovascular events, hospitalizations, and deaths compared with gels. Patches and gels had similar risk profiles. However, this study did not assess whether patients met criteria for use of testosterone and did not assess the safety of testosterone among users compared with nonusers of the drug.
An improved technique in porosity prediction: a neural network approach

Genetic reservoir characterization is important in developing, for a given petroleum reservoir, an improved understanding of the total amount and fluid flow properties of hydrocarbon reserves. Application of genetic concepts involves the classification of well log data into different lithofacies groups, followed by a facies-by-facies description of rock properties such as porosity and permeability. This work contrasts the genetic and nongenetic approaches in predicting porosity values of an oil well using backpropagation neural network methods. The performance of both methods are critically evaluated. A systematic technique to optimise the network configuration using weight visualization curves is proposed, thereby enabling the amount of training time to be significantly reduced. In the example problem, the genetic approach provides superior porosity estimates to that based on a nongenetic approach. >
Explainable Biomedical Recommendations via Reinforcement Learning Reasoning on Knowledge Graphs

For Artiﬁcial Intelligence to have a greater impact in biology and medicine, it is crucial that recommendations are both accurate and transparent. In other domains, a neurosymbolic approach of multi-hop reasoning on knowledge graphs has been shown to produce transparent explanations. However, there is a lack of research applying it to complex biomedical datasets and problems. In this paper, the approach is explored for drug discovery to draw solid conclusions on its applicability. For the ﬁrst time, we systematically apply it to multiple biomedical datasets and recommendation tasks with fair benchmark comparisons. The approach is found to outperform the best baselines by 21.7% on average whilst producing novel, biologically relevant explanations.
Results of local excision for rectal carcinoma.

OBJECTIVE To determine the results peranal excision for rectal carcinoma. DESIGN Retrospective case series. SETTING A university-affiliated hospital. PATIENTS Of 178 patients who presented for curative resection of rectal carcinoma between 1975 and 1993, 19 (10.7%) were deemed suitable for local excision. There were 10 men and 9 women with a mean age of 71.2 years. The follow-up ranged from 13 to 184 months. INTERVENTION Peranal excision. MAIN OUTCOME MEASURES Histologic differentiation, gross morphology, depth of invasion and size of the carcinoma, adequacy of margins of excision, complications of operation, rates of recurrence, results of salvage therapy and 5-year survival. RESULTS There were no intraoperative complications. Postoperative complications included urinary retention (one patient) and bleeding (one patient). There were five local recurrences (26%). Salvage operations were performed in three (60%) patients and were successful in two of them. The 5-year cancer-specific survival rate was 82%. The recurrence rate was higher in patients with inadequate margins of excision and ulcerative lesions. Neither size nor grade of the carcinoma correlated with recurrence. CONCLUSIONS Local excision of rectal carcinoma can be performed successfully in selected patients. Diligent follow-up is required, because up to 60% of local recurrences can be treated successfully.
Immediate implant placement with transmucosal healing in areas of aesthetic priority. A multicentre randomized-controlled clinical trial I. Surgical outcomes.

OBJECTIVES To compare the clinical outcomes of standard, cylindrical, screw-shaped to novel tapered, transmucosal (Straumann Dental implants immediately placed into extraction sockets. MATERIAL AND METHODS In this randomized-controlled clinical trial, outcomes were evaluated over a 3-year observation period. This report deals with the need for bone augmentation, healing events, implant stability and patient-centred outcomes up to 3 months only. Nine centres contributed a total of 208 immediate implant placements. All surgical and post-surgical procedures and the evaluation parameters were discussed with representatives of all centres during a calibration meeting. Following careful luxation of the designated tooth, allocation of the devices was randomly performed by a central study registrar. The allocated SLA titanium implant was installed at the bottom or in the palatal wall of the extraction socket until primary stability was reached. If the extraction socket was >or=1 mm larger than the implant, guided bone regeneration was performed simultaneously (Bio Oss and BioGide. The flaps were then sutured. During non-submerged transmucosal healing, everything was done to prevent infection. At surgery, the need for augmentation and the degree of wound closure was verified. Implant stability was assessed clinically and by means of resonance frequency analysis (RFA) at surgery and after 3 months. Wound healing was evaluated after 1, 2, 6 and 12 weeks post-operatively. RESULTS The demographic data did not show any differences between the patients receiving either standard cylindrical or tapered implants. All implants yielded uneventful healing with 15% wound dehiscences after 1 week. After 2 weeks, 93%, after 6 weeks 96%, and after 12 weeks 100% of the flaps were closed. Ninety percent of both implant designs required bone augmentation. Immediately after implantation, RFA values were 55.8 and 56.7 and at 3 months 59.4 and 61.1 for cylindrical and tapered implants, respectively. Patient-centred outcomes did not differ between the two implant designs. However, a clear preference of the surgeon's perception for the appropriateness of the novel-tapered implant was evident. CONCLUSIONS This RCT has demonstrated that tapered or standard cylindrical implants yielded clinically equivalent short-term outcomes after immediate implant placement into the extraction socket.
Income Effects of Training on Rural Labors

The paper analyzes income effects of training on rural labors by applying propensity score-matching method to their low earnings problem.The results show that both pre-job training and the job training can increase rural labors' earnings,especially the effect of the former is more obviously.Therefore,the government should make reasonable the training policy for rural labors to effectively increase their income.
CURRENT ISSUES IN PEDIATRIC LUPUS NEPHRITIS: ROLE OF REVISED HISTOPATHOLOGICAL CLASSIFICATION

Childhood-onset systemic lupus erythematosus (SLE) has an unpredictable natural history with variable clinical manifestations. The prognosis of SLE is linked closely to renal involvement with lupus nephritis (LN), which is more severe in patients with childhood-onset compared with adult-onset disease. The histopathological classification of LN facilitates treatment decisions, protocols, and clinical research. After the World Health Organization and modified WHO classifications of LN from 1974 to 1995, the International Society of Nephrology and Renal Pathology Society Working Group revised the histopathological classification of LN. The reclassification was published in 2004 after their consensus conference held at Columbia University in New York in May 2002. The aims of the reclassification were to standardize definitions, emphasize clinically relevant lesions, and encourage uniform and reproducible reporting among centers. Although the revised classification is time-consuming, it is important for future international collaboration on multicenter trials of disease-modifying agents. The prognosis of SLE and LN is linked to the histopathology of the renal lesion, but the clinical manifestations of LN, including nephrotic syndrome and hypertension, cannot predict the degree of renal involvement. However, we are many years away from completely understanding the etiopathogenesis of LN and the predictive role of the revised histological classification for direction of patient management.
Analysis of Human Endogenous Retrovirus Expression in Multiple Sclerosis Plaques

Background It has been suggested that Human endogenous retroviruses (HERVs) are associated with multiple sclerosis (MS) pathogenesis. The objective of this study was to broadly evaluate the expression of HERV core (GAG) and envelope (ENV) genes in diseased brain white matter samples from MS patients compared to normal controls. Methods Twenty-eight HERV GAG and 88 ENV gene sequences were retrieved, classified by phylogeny, and grouped into clades. Consensus qPCR primers were designed for each clade, and quantitative PCR was performed on 33 MS and 9 normal control frozen brain samples. MS samples included chronic progressive (n=5), primary progressive (n=4), secondary progressive (n=14), relapsing remitting (n=3) and unclassified confirmed MS cases (n=7). The levels of GAG and ENV RNA within each of the samples were quantitated and normalized using the neuronal reference gene RPL19. Expression differences were analyzed for MS vs control. Results Expression of GAG clades 1A, 3B, and 3C mapping to HERV-E and HERV-K were significantly increased compared to controls, while GAG clade 3A expression was decreased. Expression of HERV ENV clades 2, 3A, 3B, mapping to RTVL, HERV-E and HERV-K and MSRV (HERV-W), were significantly increased in the MS group. However, the relative expression differences between the MS and control groups were small, differing less than 1.5-fold. Conclusion Expression of GAG and ENV mapping to HERV-E, RTVL and HERV-K10 families were significantly increased in the MS group. However, the relative expression differences between the MS and control groups were small, differing less than 1.5-fold. These results indicate that the expression of HERV GAG and ENV regions do not differ greatly between MS and controls in these frozen brain samples.