Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Data Analysis in Obstructive Sleep Apnea

Obstructive Sleep Apnea (OSA) is a serious disease caused by the collapse of upper airways during sleep. The present method of measuring the severity of OSA is the Apnea Hypopnea Index (AHI). The AHI is defined as the average number of Obstructive events (Apnea and Hypopnea, OAH-events) during the total sleep period. The number of occurrence of OAH events during each hour of sleep is a random variable with an unknown probability density function. Thus the measure AHI alone is insufficient to describe its true nature. We propose a new measure Dynamic Apnea Hypopnea Index Time Series (DAHI), which captures the temporal density of Apnea event over shorter time intervals, and use its higher moments to obtain a dynamic characterization of OSA
High Degree of HIV-1 Group M (HIV-1M) Genetic Diversity within Circulating Recombinant Forms: Insight into the Early Events of HIV-1M Evolution

ABSTRACT The existence of various highly divergent HIV-1 lineages and of recombination-derived sequence tracts of indeterminate origin within established circulating recombinant forms (CRFs) strongly suggests that HIV-1 group M (HIV-1M) diversity is not fully represented under the current classification system. Here we used a fully exploratory screen for recombination on a set of 480 near-full-length genomes representing the full known diversity of HIV-1M. We decomposed recombinant sequences into their constituent parts and then used maximum-likelihood phylogenetic analyses of this mostly recombination-free data set to identify rare divergent sequence lineages that fall outside the major named HIV-1M taxonomic groupings. We found that many of the sequence fragments occurring within CRFs (including CRF04_cpx, CRF06_cpx, CRF11_cpx, CRF18_cpx, CRF25_cpx, CRF27_cpx, and CRF49_cpx) are in fact likely derived from divergent unclassified parental lineages that may predate the current subtypes, even though they are presently identified as derived from currently defined HIV-1M subtypes. Our evidence suggests that some of these CRFs are descended predominantly from what were or are major previously unidentified HIV-1M lineages that were likely epidemiologically relevant during the early stages of the HIV-1M epidemic. The restriction of these divergent lineages to the Congo basin suggests that they were less infectious and/or simply not present at the time and place of the initial migratory wave that triggered the global epidemic. IMPORTANCE HIV-1 group M (HIV-1M) likely spread to the rest of the world from the Congo basin in the mid-1900s (N. R. Faria et al., Science 346:56–61, 2014, http://dx.doi.org/10.1126/science.1256739) and is today the principal cause of the AIDS pandemic. Here, we show that large sequence fragments from several HIV-1M circulating recombinant forms (CRFs) are derived from divergent parental lineages that cannot reasonably be classified within the nine established HIV-1M subtypes. These lineages are likely to have been epidemiologically relevant in the Congo basin at the onset of the epidemic. Nonetheless, they appear not to have undergone the same explosive global spread as other HIV-1M subtypes, perhaps because they were less transmissible. Concerted efforts to characterize more of these divergent lineages could allow the accurate inference and chemical synthesis of epidemiologically key ancestral HIV-1M variants so as to directly test competing hypotheses relating to the viral genetic factors that enabled the present pandemic.
Adiabatic population transfer in a multilevel system.

We report an experimental observation of coherent population transfer in a multilevel system by adiabatic following through a trapped state. Raman transitions between ground-state sublevels are induced by two partially overlapping a± polarized laser beams, tuned to the hyperfine transition F=4→F'=4 of the cesium D 2 line. An efficiency of more than 50% is observed for the m F =+4→m F =-4 population transfer. The influence of other excited hyperfine levels on the transfer efficiency is pointed out. The feasibility of the technique with counterpropagating laser beams is also demonstrated
Application of Oxidation-Reduction Assay for Monitoring Treatment of Patients with Pulmonary Tuberculosis

ABSTRACT By oxidation-reduction assay, the viability of Mycobacterium tuberculosis in sputum specimens was evaluated. The technique is based on the Alamar Blue and Malachite Green dyes, which change their color in response to M. tuberculosis growth. The method is simple, permits visual reading of results, and is applicable for laboratories with limited resources.
A fast start-up 3GHz–10GHz digitally controlled oscillator for UWB impulse radio in 90nm CMOS

A digitally controlled ring oscillator, key component of a UWB transceiver, is presented. The design supports the IEEE 802.15. 4 standard for which all bands between 3 and 10 GHz can be synthesized with frequency steps as small as 4 MHz, it is to be embedded in a low power fast startup phase- aligned frequency-locked loop requiring a duty-cycled operation of the DCO with a settling time below 2 ns. The average power consumption ranges from 0.3 mW at 3 GHz up to 1 mW at 10 GHz in 90 nm IV digital CMOS.
Influences of dynamic factors on myoelectric parameters.

We present a compilation of results from previous studies and preliminary results from a new study all conducted by the authors describing the influences of joint angle and muscle force on two myoelectric parameters-conduction velocity and the mean frequency (MF) of the power spectrum. Also described is an estimation technique that significantly diminishes the effects on MF estimation during dynamic muscle contractions.
Do Insurers Risk-Select Against Each Other? Evidence from Medicaid and Implications for Health Reform

Increasingly in U.S. public insurance programs, the state finances and regulates competing, capitated private health plans but does not itself directly insure beneficiaries through a public fee-for-service (FFS) plan. We develop a simple model of risk-selection in such settings. Capitation incentivizes insurers to retain low-cost clients and thus improve their care relative to high-cost clients, who they prefer would switch to a competitor. We test this prediction using county transitions from FFS Medicaid to capitated Medicaid managed care (MMC) for pregnant women and infants. We first document the large health disparities and corresponding cost differences between blacks and Hispanics (who make up the large majority of Medicaid enrollees in our data), with black births costing nearly double that of Hispanics. Consistent with the model, black-Hispanic infant health disparities widen under MMC (e.g., the black-Hispanic mortality gap grows by 42 percent) and black mothers' pre-natal care worsens relative to that of Hispanics. Remarkably, black birth rates fall (and abortions rise) significantly after MMC--consistent with mothers reacting to poor care by reducing fertility or plans discouraging births from high-cost groups. Implications for the ACA exchanges are discussed
Intensive chemotherapy and immunotherapy in patients with newly diagnosed primary CNS lymphoma: CALGB 50202 (Alliance 50202).

PURPOSE Concerns regarding neurocognitive toxicity of whole-brain radiotherapy (WBRT) have motivated development of alternative, dose-intensive chemotherapeutic strategies as consolidation in primary CNS lymphoma (PCNSL). We performed a multicenter study of high-dose consolidation, without WBRT, in PCNSL. Objectives were to determine: one, rate of complete response (CR) after remission induction therapy with methotrexate, temozolomide, and rituximab (MT-R); two, feasibility of a two-step approach using high-dose consolidation with etoposide plus cytarabine (EA); three, progression-free survival (PFS); and four, correlation between clinical and molecular prognostic factors and outcome. PATIENTS AND METHODS Forty-four patients with newly diagnosed PCNSL were treated with induction MT-R, and patients who achieved CR received EA consolidation. We performed a prospective analysis of molecular prognostic biomarkers in PCNSL in the setting of a clinical trial. RESULTS The rate of CR to MT-R was 66%. The overall 2-year PFS was 0.57, with median follow-up of 4.9 years. The 2-year time to progression was 0.59, and for patients who completed consolidation, it was 0.77. Patients age > 60 years did as well as younger patients, and the most significant clinical prognostic variable was treatment delay. High BCL6 expression correlated with shorter survival. CONCLUSION CALGB 50202 demonstrates for the first time to our knowledge that dose-intensive consolidation for PCNSL is feasible in the multicenter setting and yields rates of PFS and OS at least comparable to those of regimens involving WBRT. On the basis of these encouraging results, an intergroup study has been activated comparing EA consolidation with myeloablative chemotherapy in this randomized trial in PCNSL, in which neither arm involves WBRT.
OKSAT at NTCIR-11 RecipeSearch: Categorization and Expansion of Search Terms in Topics

Our group OKSAT submitted five runs for English and Japanese ad hoc recipe search (EN1 and JA1) subtasks of NTCIR-11 Cooking Recipe Search (RecipeSearch). For EN1, we tried to categorize search terms of topics. We also tried to expand search term for some runs we submitted. Analyzing experimental results, we observe the effectiveness of our method.
Chronic respiratory diseases.

If this is true of diet and smoking it is even more true of the social environment: housing, the nature or work, education, social relationships. The research agenda for public health now should not only ask how best to achieve change in unhealthy behaviours but how to identify the social and economic causes of ill health, whether they act by affecting behaviours or by other means related to the environment; whether they act in adulthood or whether they act early in life. 16s18 Rose's insight on blood pressure and cholesterol applies also to social differences in ill health. People at the lower end of the social distribution, the poor, the homeless and the unemployed, have worse health than those better off. But although these individuals are at high risk and require attention, they are
An intensivist-directed intensive care unit improves clinical outcomes in a combat zone

Objective: Intensivist-directed intensive care units (ICUs) have been shown to improve clinical outcomes. Numerous barriers exist that limit hospitals adopting this practice. We sought to show this staffing model can be implemented in an austere environment with limited resources resulting in improved outcomes. Design: We conducted a retrospective observational cohort study of consecutive adult patients admitted to the ICU between March 2004 and January 2007. Setting: This study was conducted in an ICU in a U.S. Army Combat Support Hospital deployed to Afghanistan. Patients: North Atlantic Trade Organization members (U.S. military service members, American civilian contractors, members of the North Atlantic Trade Organization Coalition International Security Assistance Force), members of the Afghanistan National Army and National Police, and local Afghani nationals were included in the study. Both traumatic injuries and medical illnesses were treated. Interventions: During the observation period, the ICU was converted from an open model to an intensivist-directed model. Measurements and Main Results: Outcomes compared between the two models included ICU and hospital mortality, duration of mechanical ventilation, and ventilator-associated pneumonia rates. During the observation period, there were 2740 admissions, 965 of which were initially admitted to the ICU. We found significant reductions in ICU mortality (6.6% vs. 4.0%, p < 0.001), duration of mechanical ventilation (4.7 ± 3.9 days vs. 3.1 ± 2.7 days, p < 0.001), and rates of ventilator-associated pneumonia (42.5% vs. 8.0%; p < 0.001). Conclusions: Transition to an intensivist-directed ICU in an Army Combat Support Hospital improved outcomes among ICU patients. This study demonstrates the feasibility of using this model in an austere, combat environment.
Fuzzy Knowledge-based Image Annotation Refinement

Automatic image annotation methods automatically assign labels to images in order to facilitate tasks such as image retrieval. Incorrect labels may negatively influence the search results so image annotation should be as accurate as possible. Labels pertaining to objects or to whole scenes are commonly used for image annotation, and precision is especially important in case when scene labels are inferred from objects, as errors in the object labels may propagate to the scene level. To improve the annotation precision, the idea is to infer which labels are incorrect using the context of other labels and the knowledge about objects and their relations. This procedure is here referred to as annotation refinement. The proposed approach used in this paper includes a fuzzy knowledge base and uses the fuzzy inference algorithms to detect and discard automatically obtained object labels that do not fit the context of other detected objects.
Acute coronary syndromes: unstable angina and non-Q-wave myocardial infarction.

Ischemic heart disease includes a wide spectrum of conditions, ranging from silent ischemia and exertion-induced angina, through unstable angina, to acute MI. Unstable angina occupies the center of this spectrum, causing disability and risk greater than that of chronic stable angina but less than that of acute MI1 (Fig 1⇓). Although non–Q-wave MI for many years was considered prognostically similar to unstable angina, recent longitudinal studies indicate that it is similar to Q-wave infarction2 3 (Fig 2⇓). Figure 1. Cumulative 6-month mortality from ischemic heart disease. Diagnosis on admission to hospital (n=21 761; 1985 to 1992). From Duke Cardiovascular Database. Reproduced with permission from Reference 1. Figure 2. Top, Cumulative 1-year combined death or MI among patients with Q-wave and non–Q-wave MI treated with fibrinolysis. Reproduced with permission from Reference 2. Bottom, Risk of subsequent cardiac events in stable convalescing patients after first non–Q-wave and Q-wave MI. Reproduced with permission from Reference 3. The concept of unstable angina has emerged from observations of frequent symptoms preceding acute MI, followed by prospective documentation that unstable symptoms frequently culminated in acute MI. The syndrome was rapidly accepted as a well-defined clinical entity as specific clinical manifestations, pathophysiological mechanisms, laboratory findings, and treatment became better characterized. Unstable angina is currently one of the leading causes of hospital admission for CAD, and non–Q-wave MI accounts for >30% of admissions for acute MI.1 4 Yet, the diagnosis of unstable angina remains clinical, based on symptom recognition. The physician caring for patients with unstable angina is in a privileged position of recognizing rapidly evolving CAD and being able to intervene to prevent irreversible left ventricular damage and progression of CAD. Unstable angina is classically described as a heterogeneous disease, referring to a wide spectrum of clinical manifestations from stable angina to MI, of disease …
A Note on (Parallel) Depth- and Breadth-First Search by Arc Elimination

This note recapitulates an algorithmic observation for ordered Depth-First Search (DFS) in directed graphs that immediately leads to a parallel algorithm with linear speed-up for a range of processors for non-sparse graphs. The note extends the approach to ordered Breadth-First Search (BFS). With $p$ processors, both DFS and BFS algorithms run in $O(m/p+n)$ time steps on a shared-memory parallel machine allowing concurrent reading of locations, e.g., a CREW PRAM, and have linear speed-up for $p\leq m/n$. Both algorithms need $n$ synchronization steps.
Do Mergers Really Reduce Costs? Evidence from Hospitals

In this paper, we compare potential and realized cost savings from hospital mergers. Our approach isolates changes in realized cost savings due to different output mixes from systematic changes due to time and also provides a measure of the potential cost savings due to scale economies. Our findings suggest that economies of scale are present for merging hospitals and they realize these cost savings immediately following a merger. However, we also show that over time, cost savings from the merger decrease and the proportion of hospitals experiencing positive cost savings declines.
Predicting Pulmonary Function from Phone Sensors

Abstract Introduction: Smartphones are ubiquitous, but it is unknown what physiological functions can be monitored at clinical quality. Pulmonary function is a standard measure of health status for cardiopulmonary patients. We have shown phone sensors can accurately measure walking patterns. Here we show that improved classification models can accurately predict pulmonary function, with sole inputs being motion sensors from carried phones. Subjects and Methods: Twenty-five cardiopulmonary patients performed 6-minute walk tests in pulmonary rehabilitation at a regional hospital. They carried smartphones running custom software recording phone motion. Each patient's pulmonary function was measured by spirometry. A universal model, based on support vector machine, then computed the category of function with input from signal processing features and patient demographic features. Results: All but a few of every 10-second interval for every patient was correctly predicted. The trained model perfectly computed the GOLD (Global Initiative for Chronic Obstructive Lung Disease) level 1/2/3, which is a standard classification of pulmonary function. Each level was determined to have a characteristic motion, which could be recognized from the sensor features. In addition, longitudinal changes were detected for 10 patients with multiple walk tests, except for cases with clinical instability. Conclusions: These results are encouraging toward clinical validation of passive monitors running continuously in the background, for patients in homes during daily activities. Initial testing indicates the same high accuracy as with active monitors, for patients in hospitals during walk tests. We expect patients can simply carry their phones during everyday living, while models support automatic prediction of pulmonary function for health monitoring.
Scale-space clustering and classification of SAR images with numerous attributes and classes

Describes application of scale-space clustering to the classification of a multispectral and polarimetric SAR image of an agricultural site. After polarimetric and radiometric calibration and noise cancellation, the authors extracted a 12-dimensional feature vector for each pixel from the scattering matrix. The algorithm was able to partition without supervision a set of unlabeled vectors from 13 selected sites, each site corresponding to a distinct crop, into 13 clusters. The cluster parameters were then used to classify the whole image. The classification map is much less noisy and more accurate than those obtained by hierarchical rules. The algorithm can handle variabilities in cluster densities, cluster sizes and ellipsoidal shapes. <<ETX>>
The Receptor Kinase CORYNE of Arabidopsis Transmits the Stem Cell–Limiting Signal CLAVATA3 Independently of CLAVATA1[W]

Stem cells in shoot and floral meristems of Arabidopsis thaliana secrete the signaling peptide CLAVATA3 (CLV3) that restricts stem cell proliferation and promotes differentiation. The CLV3 signaling pathway is proposed to comprise the receptor kinase CLV1 and the receptor-like protein CLV2. We show here that the novel receptor kinase CORYNE (CRN) and CLV2 act together, and in parallel with CLV1, to perceive the CLV3 signal. Mutations in CRN cause stem cell proliferation, similar to clv1, clv2, and clv3 mutants. CRN has additional functions during plant development, including floral organ development, that are shared with CLV2. The CRN protein lacks a distinct extracellular domain, and we propose that CRN and CLV2 interact via their transmembrane domains to establish a functional receptor.
Partial amino-acid sequence of human PMN leukocyte procollagenase.

: Human PMN leukocyte procollagenase was purified to apparent homogeneity using ion exchange chromatography on Q-Sepharose Fast Flow, affinity chromatography on Zinc Chelate Sepharose and on Orange Sepharose and was finally purified by gelpermeation chromatography on Sephacryl S-300. It was shown by SDS-PAGE under reducing and non-reducing conditions that PMNL procollagenase consists of a single polypeptide chain with an apparent Mr 85000. Amino acid sequence information was obtained from the proenzyme and fragments by Edman degradation and showed that PMNL procollagenase is homologous to the fibroblast enzyme. Thus PMNL procollagenase is the product of an independent gene.
Elevated Admission Base Deficit Is Associated with a Complex Dynamic Network of Systemic Inflammation Which Drives Clinical Trajectories in Blunt Trauma Patients

We hypothesized that elevated base deficit (BD) ≥ 4 mEq/L upon admission could be associated with an altered inflammatory response, which in turn may impact differential clinical trajectories. Using clinical and biobank data from 472 blunt trauma survivors, 154 patients were identified after excluding patients who received prehospital IV fluids or had alcohol intoxication. From this subcohort, 84 patients had a BD ≥ 4 mEq/L and 70 patients with BD < 4 mEq/L. Three samples within the first 24 h were obtained from all patients and then daily up to day 7 after injury. Twenty-two cytokines and chemokines were assayed using Luminex™ and were analyzed using two-way ANOVA and dynamic network analysis (DyNA). Multiple mediators of the innate and lymphoid immune responses in the BD ≥ 4 group were elevated differentially upon admission and up to 16 h after injury. DyNA revealed a higher, sustained degree of interconnectivity of the inflammatory response in the BD ≥ 4 patients during the initial 16 h after injury. These results suggest that elevated admission BD is associated with differential immune/inflammatory pathways, which subsequently could predispose patients to follow a complicated clinical course.
Lower Bounds in Lot-Sizing Models: A Polyhedral Study

Variable lower bounds in Mixed Integer Programs are constraints with the general form xâ¥Ly,where xis a continuous variable and y is a binary or an integer variable. This type of constraints is present in some Lot-Sizing models, where x represents the amount of some article produced by a machine and y∈{0,1}indicates whether the machine is set-up for that articley = 1 or not y = 0. In these models, production below some level is not allowed, in order to make full use of resources. In this paper we study, from the polyhedral viewpoint, the mixed integer models whose feasible set includes an additive constraint Σxj â¤â¥, =D, and constraints Lyj â¤ xj â¤ Kyj, where xj are continuous variables, yj are integer or binary variables, and K is a large constant. We derive families of strong valid inequalities and show they are sufficient to describe completely the convex hulls of the sets of feasible solutions. Moreover, we develop polynomial algorithms to solve the separation problem associated to each of the families obtained. Finally, we incorporate the inequalities obtained in a cutting plane algorithm, and test their ability to solve some multi-item lot-sizing problems.