Miracle-dz/UniFAR-FTUs huggingface dataset:
gd T Cells from Tolerized ab T Cell Receptor ( TCR ) – deficient Mice Inhibit Contact Sensitivity-Effector T Cells In Vivo , and Their Interferon-g Production In Vitro

From the * Department of Immunology, College of Medicine, Jagiellonian University, Krakow, Poland; ‡ Section of Allergy and Clinical Immunology, Dept. of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520-8013; § Department of Biology and Section of Immunobiology, Kline Biology Tower, Yale University, New Haven, Connecticut 06520; and i Imperial Cancer Research Foundation, London, England WZCA 3PX
Integration of Inventory and Pricing Decisions with Costly Price Adjustments

Motivated by the widespread adoption of dynamic pricing in industry and the empirical evidence of costly price adjustments, in this paper we consider a periodic-review inventory model with price adjustment costs that consist of both fixed and variable components. In each period, demand is stochastic and price-dependent. The firm needs to coordinate the pricing and inventory replenishment decisions in each period to maximize its total discounted profit over a finite planning horizon. We develop the general model and characterize the optimal policies for two special scenarios, namely, a model with inventory carryover and no fixed price-change costs and a model with fixed price-change costs and no inventory carryover. Finally, we propose an intuitive heuristic policy to tackle the general system whose optimal policy is expected to be very complicated. Our numerical studies show that this heuristic policy performs well.
Cancer Patients Role of Antitumor Activity of Alveolar Macrophages in Lung Updated

The purpose of this study is to clarify the significance of antitumor activity of alveolar macrophages (AM) in lung cancer patients. AM from tumor-bearing and non-tumor-bearing segments were obtained separately by the lavage of bronchoalveolar tracts of resected lungs of 74 patients with primary lung cancer. Cytostatic activity (CIS) of AM obtained from non-tumor-bearing segments was stable in spite of enlargement of tumor size or progression of N factor. In contrast, ("IS of AM obtained from tumor-bearing segments may be augmented at Stage II as compared with Stage I, and suppressed with an advance of stage from II through IV, although the number of Stage II patients was as small as three. Moreover, ("IS of AM from tumor-bearing segments was suppressed in V as compared with No or Nt, and also it was suppressed as compared with that of AM from non-tumor-bearing segments in N2 disease. ("IS of AM from smokers was suppressed as compared with that of nonsmokers in both tumor-bearing and non-tumor-bearing segments. These results sug gest that lung cancer cells or their products may suppress antitumor activity of AM in the tumor-bearing segments at advanced stages, and cigarette smoking is a suppressive factor on antitumor activity of AM.
Temporal Fluctuation of Multidrug Resistant Salmonella Typhi Haplotypes in the Mekong River Delta Region of Vietnam

Background Typhoid fever remains a public health problem in Vietnam, with a significant burden in the Mekong River delta region. Typhoid fever is caused by the bacterial pathogen Salmonella enterica serovar Typhi (S. Typhi), which is frequently multidrug resistant with reduced susceptibility to fluoroquinolone-based drugs, the first choice for the treatment of typhoid fever. We used a GoldenGate (Illumina) assay to type 1,500 single nucleotide polymorphisms (SNPs) and analyse the genetic variation of S. Typhi isolated from 267 typhoid fever patients in the Mekong delta region participating in a randomized trial conducted between 2004 and 2005. Principal Findings The population of S. Typhi circulating during the study was highly clonal, with 91% of isolates belonging to a single clonal complex of the S. Typhi H58 haplogroup. The patterns of disease were consistent with the presence of an endemic haplotype H58-C and a localised outbreak of S. Typhi haplotype H58-E2 in 2004. H58-E2-associated typhoid fever cases exhibited evidence of significant geo-spatial clustering along the Sông H u branch of the Mekong River. Multidrug resistance was common in the established clone H58-C but not in the outbreak clone H58-E2, however all H58 S. Typhi were nalidixic acid resistant and carried a Ser83Phe amino acid substitution in the gyrA gene. Significance The H58 haplogroup dominates S. Typhi populations in other endemic areas, but the population described here was more homogeneous than previously examined populations, and the dominant clonal complex (H58-C, -E1, -E2) observed in this study has not been detected outside Vietnam. IncHI1 plasmid-bearing S. Typhi H58-C was endemic during the study period whilst H58-E2, which rarely carried the plasmid, was only transient, suggesting a selective advantage for the plasmid. These data add insight into the outbreak dynamics and local molecular epidemiology of S. Typhi in southern Vietnam.
Convergence of an Alternating Maximization Procedure

We derive two convergence results for a sequential alternating maximization procedure to approximate the maximizer of random functionals such as the realized log likelihood in MLE estimation. We manage to show that the sequence attains the same deviation properties as shown for the profile M-estimator by Andresen and Spokoiny (2013), that means a finite sample Wilks and Fisher theorem. Further under slightly stronger smoothness constraints on the random functional we can show nearly linear convergence to the global maximizer if the starting point for the procedure is well chosen.
Diffusional Kurtosis Imaging in Acute Human Stroke

The management of acute human stroke is a high-priority medical emergency. Thrombolytic therapy is now part of the standard of care in most major medical centers, and the selection of patients for these treatments depends on several clinical factors as well as brain imaging findings. Diffusion MRI combined with perfusion imaging are accepted imaging protocols used to characterize ischemic stroke and a perfusion-diffusion mismatch has proven clinically important for the triage of patients for thrombolytic therapy. However, variability in the experimental methodology and analysis of the data as well as in the specific criteria used for interpreting the perfusion/diffusion mismatch are not without controversy. The most commonly used diffusion MRI images employed in the characterization of stroke include DWI and the calculated ADC maps. It has long been appreciated, however, that diffusion-weighted MRI is, in principle, capable of yielding considerably more information about the state of tissue than what is derived from presently implemented diffusion methods. Diffusional Kurtosis Imaging (DKI) is a relatively new MRI technique [1-3] for quantifying non-Gaussian water diffusion. Importantly, it is clinically a more practical technique (compared with, e.g., q-space imaging) with acceptable image acquisition times that can be easily implemented on clinical scanners using vendor-provided commercial software. From DKI, one can calculate all of the conventional diffusion metrics as well as a new metric, the mean kurtosis (MK). The MK measures a fundamentally different aspect of the diffusion process, is meaningful in both grey and white matter, and is relatively impervious to CSF partial volume affects. As a consequence, MK may be a more specific marker of tissue microstructural integrity. In this work, we present preliminary results of DKI applied to human ischemic stroke.
Efficient Learning-based Image Enhancement: Application to Super-resolution and Compression Artifact Removal

In this paper, we describe a framework for learning-based image enhancement. At the core of our algorithm lies a generic regularization framework that comprises a prior on natural images, as well as an application-specific conditional model based on Gaussian processes. In contrast to prior learning-based approaches, our algorithm can instantly learn task-specific degradation models from sample images which enables users to easily adopt the algorithm to a specific problem and data set of interest. This is facilitated by our efficient approximation scheme of large-scale Gaussian processes. We demonstrate the efficiency and effectiveness of our approach by applying it to two example enhancement applications: single-image super-resolution as well as artifact removal in JPEG-encoded images.
Applications of variational analysis to a generalized Heron problem

This article is a continuation of our ongoing efforts to solve a number of geometric problems and their extensions by using advanced tools of variational analysis and generalized differentiation. Here we propose and study, from both qualitative and numerical viewpoints, the following optimal location problem as well as its further extensions: on a given nonempty subset of a Banach space, find a point such that the sum of the distances from it to n given nonempty subsets of this space is minimal. This is a generalized version of the classical Heron problem: on a given straight line, find a point C such that the sum of the distances from C to the given points A and B is minimal. We show that the advanced variational techniques allow us to solve optimal location problems of this type completely in some important settings.
Identifying Tasks and Predicting Action in Smart Homes using Unlabeled Data

An intelligent home is likely in the near future. An important ingredient in an intelligent environment such as a home is prediction – of the next low-level action, the next location, and the next high-level task that an inhabitant is likely to perform. In this paper we model inhabitant actions as states in a simple Markov model. We introduce an enhancement, the Taskbased Markov model (TMM) method. TMM discovers high-level inhabitant tasks using the unlabeled data supplied. We investigate clustering of actions to identify tasks, and integrate clusters into a hidden Markov model that predicts the next inhabitant action. We validate our approach and observe that for simulated data we achieve good accuracy using both the simple Markov model and the TMM, whereas on real data we see that simple Markov models outperform the TMM. We also perform an analysis of the performance of the HMM in the framework of the TMM when diverse patterns are introduced into the data.
Gestation Time-Dependent Pharmacokinetics of Intravenous (+)-Methamphetamine in Rats

We tested the hypothesis that differences in (+)-methamphetamine (METH) disposition during late rat pregnancy could lead to increased vulnerability to acute METH effects. The disposition of a single 1 mg/kg i.v. METH dose was studied during early (gestation day 7, GD7) and late (GD21) gestation. Results showed gestation time-dependent pharmacokinetics, characterized by a significantly higher area under the METH serum concentration versus time curve and a lower clearance on GD21 (p < 0.05; total, renal, and nonrenal clearance). The terminal elimination half-life (t1/2λz) of METH and (+)-amphetamine (AMP; a pharmacologically active metabolite of METH) were not different on GD7, but by GD21, AMP t1/2λz was 37% longer than METH t1/2λz (p < 0.05). To identify the mechanism for AMP metabolite changes, intravenous AMP pharmacokinetics on GD21 were compared with AMP metabolite pharmacokinetics after intravenous METH. The intravenous AMP t1/2λz was significantly shorter than metabolite AMP t1/2λz (p < 0.05), which suggested AMP metabolite formation (not elimination) was the rate-limiting process. To understand the medical consequence of METH use during late-stage pregnancy, timed-pregnant rats received an intravenous dose of saline or METH (1, 3, or 5.6 mg/kg) on GD21, 0 to 2 days antepartum. Although one rat died and another had stillbirths at term after the 5.6-mg/kg dose, the pharmacokinetic values for all of the other animals were not significantly different. In conclusion, late-gestational clearance reductions lengthen METH exposure time, possibly increasing susceptibility to adverse effects, including death.
Impact of Mountain Pine Beetle (MPB) Attack on Drying Characteristics of Wood

Mountain pine beetle infested lodgepole pine ( Pinus contorta var. latifolia ) containing blue stain was used for the determination of permeability and diffusion coefficients. The results were then compared with the permeability and diffusion coefficients of noninfested wood that was free from the blue stain. The comparisons indicated that the blue stain in wood significantly increased the permeability of lodgepole pine, in both tangential and radial directions. Diffusion coefficients for blue-stained sapwood were greater than those observed for nonstained sapwood.
Musculoskeletal Disorders among Dentists in Saudi Arabia

The objective of the study was to find out the prevalence and distribution of musculoskeletal symptoms among dentists in Saudi Arabia. Furthermore, to find possible correlations between these symptoms and working positions and actions. A questionnaire about musculoskeletal symptoms in different parts of the body was completed by 140 dentists (63 male, 77 female) from the public dental service clinics in Dammam and Riyadh cities. Also, a physical ergonomic examination was carried out during visiting the work places of 60 freshly graduated dentists in King Saud University College of Dentistry, Dammam Central Hospital and the Military Hospital in Al-Khobar. The following aspects were investigated: the sitting work posture, the clock-related working position, the use of dental mirror, active neck mobility and support of the left arm. The descriptive data were analyzed and chi-square test was used for statistical significance (P<.05). Eighty-three of the responding dentists had pain or discomfort from the neck, shoulders, lower back or head. Younger dentists had more symptoms than the older dentists. The female dentists had a significantly higher frequency of pain, headache and weakness than their male counterparts. Pain and headache were the most commonly reported symptoms. The dentists who use the mirror more often had less pain or discomfort in the upper locomotor system than those who do not. The analysis of the ergonomic examination showed that the most frequently used postures were posture 1 (the whole back bent, the seat straight) and posture 3 (straight lower and upper back, the neck bent, the seat straight) (46.7% and 40.0% respectively). Dentists who used posture 1 have more neck ache (25%) and lower back pain (57.1%) than those who used posture 3. No significant difference was found between male and female dentists in regard to the presence of pain (P>.05). The 10 o’clock position was the most frequently used working position by the dentists. Most of dentists supported their left arm over the left side of the head of the patient. It can be concluded that the prevalence of musculoskeletal symptoms among dentists in Saudi Arabia is high. A correlation between back pain and different work actions was observed in this investigation.
A Monte Carlo-based Model Of Gold Nanoparticle Radiosensitization

ii Acknowledgements . iv Contents . vi List of Scientific Contributions . xi Refereed Publications . xi Selected Conference Abstracts and Proceedings . xiii List of Tables . xv List of Figures . xvi List of Abbreviations . xx Chapter 1 Introduction . 1 1.1 Cancer . 2 1.1.1 Incidence, mortality, and economic burden . 2 1.1.2 Definition, etiology, and risk factors . 2 1.1.3 Treatment and management . 3 1.2 Physics of ionizing radiation . 10 vii 1.2.1 Interactions of ionizing radiation with matter . 10 1.2.2 Absorbed dose . 14 1.2. 3 Monte Carlo simulation . 15 1.3 Radiobiology . 19 1.3. 1 Radiation damage to cells . 19 1.3. 2 Radiosensitivity . 25 1.3. 3 Radiosensitization . 29 1.4 Gold nanoparticles . 33 1.4. 1 Preparation and characterization . 33 1.4. 2 AuNPs as radiosensitizers . 35 1.5 Thesis overview . 38 1.5. 1 Motivation . 38 1.5. 2 Hypothesis . 39 1.5. 3 Objectives and outline . 39 Chapter 2 A Monte Carlo approach to study the physics of gold nanoparticle radiosensitization . 64 2.1 Abstract . 65 2.2 Introduction . 66
Bacteriophage T4 UvsW protein is a helicase involved in recombination, repair and the regulation of DNA replication origins

Bacteriophage T4 UvsW protein is involved in phage recombination, repair and the regulation of replication origins. Here, we provide evidence that UvsW functions as a helicase. First, expression of UvsW allows growth of an (otherwise inviable) Escherichia coli recG rnhA double mutant, consistent with UvsW being a functional analog of the RecG helicase. Second, UvsW contains helicase sequence motifs, and a substitution (K141R) in the Walker ‘A’ motif prevents growth of the E.coli recG rnhA double mutant. Third, UvsW, but not UvsW‐K141R, inhibits replication from a T4 origin at which persistent RNA–DNA hybrids form and presumably trigger replication initiation. Fourth, mutations that inactivate UvsW and endonuclease VII (which cleaves DNA branches) synergistically block repair of double‐strand breaks. These in vivo results are consistent with a model in which UvsW is a DNA helicase that catalyzes branch migration and dissociation of RNA–DNA hybrids. In support of this model, a partially purified GST/UvsW fusion protein, but not a GST/UvsW‐K141R fusion, displays ssDNA‐dependent ATPase activity and is able to unwind a branched DNA substrate.
The Relationship of the Clinical Disc Margin and Bruch's Membrane Opening in Normal and Glaucoma Subjects

Purpose We tested the hypotheses that the mismatch between the clinical disc margin (CDM) and Bruch's membrane opening (BMO) is a function of BMO area (BMOA) and is affected by the presence of glaucoma. Methods A total of 45 normal eyes (45 subjects) and 53 glaucomatous eyes (53 patients) were enrolled and underwent radial optic nerve head (ONH) imaging with spectral domain optical coherence tomography. The inner tip of the Bruch's membrane (BM) and the clinical disc margin were marked on radial scans and optic disc photographs, and were coregistered with custom software. The main outcome measure was the difference between the clinical disc area (CDA) and BMOA, or CDA−BMOA mismatch, as a function of BMOA and diagnosis. Multivariate regression analyses were used to explore the influence of glaucoma and BMOA on the mismatch. Results Global CDA was larger than BMOA in both groups but the difference was statistically significant only in the normal group (1.98 ± 0.37 vs. 1.85 ± 0.45 mm2, P = 0.02 in the normal group; 1.96 ± 0.38 vs. 1.89 ± 0.56 mm2, P = 0.08 in the glaucoma group). The sectoral CDA−BMOA mismatch was smaller in superotemporal (P = 0.04) and superonasal (P = 0.05) sectors in the glaucoma group. The normalized CDA−BMOA difference decreased with increasing BMOA in both groups (P < 0.001). Presence or severity of glaucoma did not affect the CDA−BMOA difference (P > 0.14). Conclusions Clinical disc area was larger than BMOA in normal and glaucoma eyes but reached statistical significance only in the former group. The CDA−BMOA mismatch diminished with increasing BMOA but was not affected by presence of glaucoma. These findings have important clinical implications regarding clinical evaluation of the ONH.
Outcomes of Vaginal Prolapse Surgery Among Female Medicare Beneficiaries: The Role of Apical Support

OBJECTIVE: Recurrent pelvic organ prolapse (POP) has been attributed to many factors, one of which is lack of vaginal apical support. To assess the role of vaginal apical support and POP, we analyzed a national dataset to compare long-term reoperation rates after prolapse surgery performed with and without apical support. METHODS: Public use file data on a 5% random national sample of female Medicare beneficiaries were obtained from the Centers for Medicare and Medicaid Services. Women with POP who underwent surgery during 1999 were identified by relevant International Classification of Diseases, 9th Revision, Clinical Modification, and Current Procedural Terminology, Fourth Edition codes. Individual patients were followed-up through 2009. Prolapse repair was categorized as anterior, posterior, or anterior–posterior with or without a concomitant apical suspension procedure. The primary outcome was the rate of retreatment for POP. RESULTS: In 1999, 21,245 women had a diagnosis of POP. Of these, 3,244 (15.3%) underwent prolapse surgery that year. There were 2,756 women who underwent an anterior colporrhaphy, posterior colporrhaphy, or both with or without apical suspension. After 10 years, cumulative reoperation rates were highest among women who had an isolated anterior repair (20.2%) and significantly exceeded reoperation rates among women who had a concomitant apical support procedure (11.6%; P<.01). CONCLUSION: Ten years after surgery for POP, the reoperation rate was significantly reduced when a concomitant apical suspension procedure was performed. This analysis of a national cohort suggests that the appropriate use of a vaginal apical support procedure at the time of surgical treatment of POP might reduce the long-term risk of prolapse recurrence. LEVEL OF EVIDENCE: II
Effects of Nitric Oxide on Pseudomonas aeruginosa Infection of Epithelial Cells from a Human Respiratory Cell Line Derived from a Patient with Cystic Fibrosis

ABSTRACT Cystic fibrosis (CF) is characterized by airway inflammation and chronic bacterial lung infection, most commonly with Pseudomonas aeruginosa, an opportunistic human pathogen. Despite the persistent airway inflammation observed in patients with CF, although phagocyte inducible nitric oxide synthase (iNOS) production is upregulated, expression of iNOS in the respiratory epithelium is markedly reduced. Given the antimicrobial action of NO, this may contribute to the chronic airway infection of this disease. To define the role of epithelium-derived NO in airway defense against P. aeruginosa, we infected differentiated human bronchial epithelial cells derived from a patient with CF (CFBE41o- cells) with different strains of this pathogen at low multiplicities of infection. Using cells transfected with human iNOS cDNA, we studied the effect of NO on P. aeruginosa replication, adherence, and internalization. P. aeruginosa adherence to iNOS-expressing cells was reduced by 44 to 72% (P = 0.02) compared with control values. Absolute P. aeruginosa uptake into these cells was reduced by 44%, but uptake expressed as a percentage of adherent bacteria did not differ from the control uptake. Survival of P. aeruginosa within iNOS-expressing cells was reduced at late times postinfection (P = 0.034). NO production did not alter host cell viability. NO production reduced P. aeruginosa adherence to human bronchial epithelial cells and enhanced killing of internalized bacteria, suggesting that a lack of epithelial iNOS in patients with CF may contribute to P. aeruginosa infection and colonization.
Why I Retweet? Exploring User's Perspective on Decision-Making of Information Spreading during Disasters

The extensive use of social media during disasters raises an important issue concerning use of social media to spread information, including misinformation. This study explores the underlying behavioral context of disaster information sharing by Twitter users. We conducted a web survey with 999 respondents in Japan to determine what makes people retweet disaster information in disaster situations. As a result of factor analysis, four factors were identified from 36 questions, namely: 1) Willingness to provide relevant and updated information because the information is believable, 2) Want people to know the information they perceive as important, 3) “Retweeter” subjective feelings and interests, and 4) Want to get feedback and alert other people. The results suggest that two of the factors influenced different groups of people in the community differently; however, everybody can play their role to reduce the negative impact of social media used for future disaster. Based on the findings, we discuss practical and design implications of social media use during disasters.