Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification of changes occurring in lung patient during radiotherapy using relative γ analysis and hidden Markov models

Purpose: To present a new automated patient classification method based on relative gamma analysis and hidden Markov models (HMM) to identify patients undergoing important anatomical changes during radiation therapy. Methods: Daily EPID images of every treatment field were acquired for 52 patients treated for lung cancer. In addition, CBCT were acquired on a regular basis. Gamma analysis was performed relative to the first fraction given that no significant anatomical change was observed on the CBCT of the first fraction compared to the planning CT. Several parameters were extracted from the gamma analysis (e.g., average gamma value, standard deviation, percent above 1). These parameters formed patient‐specific time series. Data from the first 24 patients were used as a training set for the HMM. The trained HMM was then applied to the remaining 28 patients and compared to manual clinical evaluation and fixed thresholds. Results: A three‐category system was used for patient classification ranging from minor deviations (category 1) to severe deviations (category 3) from the treatment plan. Patient classified using the HMM lead to the same result as the classification made by a human expert 83% of the time. The HMM overestimate the category 10% of the time and underestimate 7% of the time. Both methods never disagree by more than one category. In addition, the information provided by the HMM is richer than the simple threshold‐based approach. HMM provides information on the likelihood that a patient will improve or deteriorate as well as the expected time the patient will remain in that state. Conclusion: We showed a method to classify patients during the course of radiotherapy based on relative changes in EPID images and a hidden Markov model. Information obtained through this automated classification can complement the clinical information collected during treatment and help identify patients in need of a plan adaptation.
Constant-Voltage-Bias Stress Testing of a-IGZO Thin-Film Transistors

Constant-voltage-bias (V<sub>DS</sub> = V<sub>GS</sub> = 30 V) stress measurements are performed for a period of 10<sup>5</sup> s on thin-film transistors (TFTs) with amorphous indium-gallium-zinc-oxide (IGZO) channel layers fabricated via RF sputtering using a postdeposition annealing temperature of 200degC, 250degC, or 300degC. Thermal silicon dioxide is employed as a TFT bottom-gate insulator. All SiO<sub>2</sub>/IGZO TFTs tested exhibit the following: 1) a positive rigid log(I<sub>D</sub>)- V<sub>GS</sub> transfer curve shift; 2) a continuous drain-current decrease over the entire stress duration; and 3) recovery of the log(I<sub>D</sub>)-V<sub>GS</sub> transfer curve toward the prestressed state when the stressed TFT is left unbiased in the dark at room temperature for an extended period of time. The SiO<sub>2</sub>/IGZO TFTs subjected to a higher postdeposition annealing temperature are more stable. A small (and typically negligible) amount of clockwise hysteresis is present in the log(I<sub>D</sub>) -V<sub>GS</sub> transfer curves of IGZO TFTs. These instability and hysteresis observations are consistent with a SiO<sub>2</sub>/ IGZO TFT instability mechanism involving electron trapping within the IGZO channel layer.
Acute cutaneous barrier disruption activates epidermal p44/42 and p38 mitogen‐activated protein kinases in human and hairless guinea pig skin

Abstract: Acute cutaneous barrier disruption of the skin elicits various homeostatic repair responses in the epidermis. Although several candidates for the signaling mechanisms that induce these responses have been reported, e.g. the calcium and ion concentration, peroxisome proliferator‐activated receptor‐α, and TNF‐α signaling mediated by sphingomyelinases, the exact nature of the signals remains undetermined. Therefore, assuming that an important group of serine/threonine‐signaling kinases, mitogen‐activated protein kinases (MAPKs), such as p44/42 MAPK, p38 MAPK, and SAPK/JNK, might link the barrier disruption to the subsequent homeostatic responses, the activation of three MAPKs in hairless guinea pig or in human skin after barrier disruption was investigated. The epidermal barrier was insulted with tape stripping or organic solvents, and the activation of these MAPKs was examined with immunohistochemistry, Western blotting, and immune complex kinase assay. In the skin of hairless guinea pigs, p44/42 MAPK and p38 MAPK, but not SAPK/JNK, were activated in epidermal keratinocytes immediately after tape stripping, and continued to be activated for at least 180 min. The activation of p44/42 MAPK was well correlated with an increase in transepidermal water loss, which was positively correlated with the number of tape strippings, whereas the covering of the stripped skin with occlusive dressing or with Ca2++ K++sucrose solution suppressed its activation. The activation of p44/42 MAPK was also induced by treatment of the skin with organic solvents. In a similar fashion, p44/42 and p38 MAPKs were found to be activated in human skin after tape stripping. These results strongly suggest that the activation of p44/42 and p38 MAPKs links the stimuli of barrier disruption to the subsequent homeostatic responses to repair the barrier defect.
Recruitment of a Foreign Quinone into the A1 Site of Photosystem I

Interruption of the menAor menB gene in Synechocystis sp. PCC 6803 results in the incorporation of a foreign quinone, termed Q, into the A1 site of photosystem I with a number of experimental indicators identifying Q as plastoquinone-9. A global multiexponential analysis of time-resolved optical spectra in the blue region shows the following three kinetic components: 1) a 3-ms lifetime in the absence of methyl viologen that represents charge recombination between P700+ and an FeS− cluster; 2) a 750-μs lifetime that represents electron donation from an FeS−cluster to methyl viologen; and 3) an ∼15-μs lifetime that represents an electrochromic shift of a carotenoid pigment. Room temperature direct detection transient EPR studies of forward electron transfer show a spectrum of P700+ Q− during the lifetime of the spin polarization and give no evidence of a significant population of P700+ FeS− fort ≤ 2–3 μs. The UV difference spectrum measured 5 μs after a flash shows a maximum at 315 nm, a crossover at 280 nm, and a minimum at 255 nm as well as a shoulder at 290–295 nm, all of which are characteristic of the plastoquinone-9 anion radical. Kinetic measurements that monitor Q at 315 nm show a major phase of forward electron transfer to the FeS clusters with a lifetime of ∼15 μs, which matches the electrochromic shift at 485 nm of the carotenoid, as well as an minor phase with a lifetime of ∼250 μs. Electrometric measurements show similar biphasic kinetics. The slower kinetic phase can be detected using time-resolved EPR spectroscopy and has a spectrum characteristic of a semiquinone anion radical. We estimate the redox potential of plastoquinone-9 in the A1site to be more oxidizing than phylloquinone so that electron transfer from Q− to F X is thermodynamically unfavorable in the menA and menB mutants.
Bayesian Shrinkage of Portfolio Weights

We propose a novel regression approach for optimizing portfolios by means of Bayesian regularization techniques. In particular, we represent the weight deviations of the global minimum variance portfolio from a reference portfolio (e.g. the naive 1/N portfolio) as coefficients of a linear regression and shrink them towards zero through Bayesian shrinkage priors. By doing so, we aim to robustify the portfolios against estimation risk. Modeling the optimal portfolio weights through Bayesian priors avoids estimating the moments of the asset return distribution and substantially reduces the dimensionality of the estimation problem. We compare the proposed Bayesian shrinkage strategies to popular frequentist approaches and find that the former show better out-of-sample performance based on various performance criteria. They also turn out to be particularly attractive for high-dimensional portfolios.
Development of a Single-Gene, Signature-Tag-Based Approach in Combination with Alanine Mutagenesis To Identify Listeriolysin O Residues Critical for the In Vivo Survival of Listeria monocytogenes

ABSTRACT Listeriolysin O (LLO) is a pore-forming toxin of the cholesterol-dependent cytolysin (CDC) family and a primary virulence factor of the intracellular pathogen Listeria monocytogenes. LLO mediates rupture of phagosomal membranes, thereby releasing bacteria into the growth-permissive host cell cytosol. Several unique features of LLO allow its activity to be precisely regulated in order to facilitate phagosomal escape, intracellular growth, and cell-to-cell spread. To improve our understanding of the multifaceted contribution of LLO to the pathogenesis of L. monocytogenes, we developed a screen that combined saturation mutagenesis and signature tags, termed i n v ivo analysis by saturation mutagenesis and signature tags (IVASS). We generated a library of LLO mutant strains, each harboring a single amino acid substitution and a signature tag, by using the previously described pPL2 integration vector. The signature tags acted as molecular barcodes, enabling high-throughput, parallel analysis of 40 mutants in a single animal and identification of attenuated mutants by negative selection. Using the IVASS technique we were able to screen over 90% of the 505 amino acids present in LLO and identified 60 attenuated mutants. Of these, 39 LLO residues were previously uncharacterized and potentially revealed novel functions of the toxin during infection. The mutants that were subsequently analyzed in vivo each conferred a 2- to 4-orders of magnitude loss in virulence compared to wild type, thereby validating the screening methods. Phenotypic analysis of the LLO mutant library using common in vitro techniques suggested that the functional contributions of some residues could only have been revealed through in vivo analysis.
Noise in acute patient care areas

This study was designed to describe the level of sound in acute patient care areas. A convenience sample of 25 subjects from four intensive care and two general care units within three hospitals in a large metropolitan area was studied. Continuous decibel levels [dB(A)] and equivalent continuous sound pressure levels [LEQ] were measured for 24 continuous hours. Two 3-hour observations were made to assess the sources of sound, and patients were interviewed to determine their perceptions of sound effects. Continuous high noise levels were found in the larger hospital's open heart recovery room and intensive care units [48.5-68.5 dB(A), 15-minute LEQ], lower levels in the smaller hospital's intensive care units [32.5-57 dB(A)] and varying levels in the general ward areas [34.25-62.5 dB(A)]. Decibel levels generated from equipment reached 90 dB(A) in some instances. Patients' perceptions ranged from content to highly perturbed. Although some sources of noise were not immediately changeable, other were adaptable, preventable, or reducible.
Direct Liquid Jet-Impingment Cooling With Micron-Sized Nozzle Array and Distributed Return Architecture

We demonstrate submerged single-phase direct liquid-jet-impingement cold plates that use arrays of jets with diameters in the range of 31 to 126 mum and cell pitches from 100 to 500 mum for high power-density microprocessor cooling applications. Using parallel inlet and outlet manifolds, a distributed return concept for easy scaling to 40,000 cells on an area of 4 cm was implemented. Pressure drops < 0.1 bar at 2.5 1/min flow rate have been reached with a hierarchical tree-like double-branching manifold. Experiments were carried out with water jets having Reynolds numbers smaller than 900 at nozzle to heater gaps ranging between 3 to 300 mum. We identified four flow regimes, namely, pinch-off, transition, impingement, and separation, with different influences on heat-removal and pressure-drop characteristics. Parametric analysis resulted in an optimal heat-removal rate of 420 W/cm2 using water as a coolant. For a near optimal design with a gap to inlet diameter ratio of 1.2, we measured a heat-transfer coefficient of 8.7 W/cm2 K and a junction to inlet fluid unit thermal resistance of 0.17 Kcm2 /W (720 mum chip), which is equivalent to a 370 W/cm2 cooling performance at a junction to inlet fluid temperature rise of 63 degC, a pressure drop of 0.35 bar, and a flow rate of 2.5 1/min
Alternative methods of cladribine administration

Nucleoside derivative cladribine treatment in hairy cell leukemia (HCL) is a rare example of treatment success in cancer. In fact, HCL is generally responsive to single-agent cladribine and only a minority of patients are refractory. Cladribine was originally administered intravenously as a continuous infusion at a dose of 0.1 mg/kg/day for 7 consecutive days. Subsequently cladribine has been administered intravenously, as a 2 h infusion for 5 consecutive days or weekly for 7 weeks, or subcutaneously. These regimens are all very effective but often show relevant toxicity. The subcutaneous route is easier to administer and may increase compliance of the patient. We have had the opportunity to investigate the efficacy and toxicity of subcutaneous cladribine given at the dose of 0.1 mg/kg/day for 5 or 7 days as a single course in newly diagnosed HCL requiring treatment, in an ongoing Italian multicenter clinical trial. Overall responses have been no different in the two arms, while a much lower infection rate was observed when cladribine was given at the lowest dose. Subcutaneous administration may be deemed a very convenient route since it does not require hospitalization. A reduced dosage of cladribine may also be advantageous since it may be associated with reduced toxicity and may set the dose needed for combinations with antibody treatments.
Gastroesophageal reflux among different racial groups in the United States.

BACKGROUND & AIMS White people in the United States are several-fold more affected by esophageal adenocarcinoma than black people. It remains unknown whether this racial discrepancy reflects a higher prevalence of gastroesophageal reflux disease (GERD) symptoms or a higher degree of esophageal damage. METHODS A cross-sectional survey followed by endoscopy was performed among employees at a VA medical center. The association between race and GERD symptoms and erosive esophagitis was analyzed in logistic regression analyses controlling for demographic, clinical, and histologic variables. RESULTS A total of 496 of 915 people (54%) returned interpretable questionnaires, and endoscopy was performed in 215 participants. The mean age was 45 years, and 336 (68%) were women. Racial distribution was 43% black, 34% white, and 23% other races. Heartburn occurring at least weekly was reported in 27%, 23%, and 24% of these racial groups, respectively. The age-adjusted prevalence of heartburn or regurgitation was not significantly different among the groups. Erosive esophagitis was found in 50 of 215 participants (23%); 31 of these cases were mild. Only one person had Barrett's esophagus (0.4%). For weekly heartburn or regurgitation, black participants had significantly less frequent erosive esophagitis than white participants (24% vs. 50%; P = 0.03). With multiple adjustments, black participants had a persistently lower risk of esophagitis (adjusted odds ratio, 0.22-0.46; P < 0.001). CONCLUSIONS White and black people in the United States have a similarly high prevalence of GERD symptoms. However, black people have a lower prevalence of esophagitis for the same frequency of GERD symptoms. Barrett's esophagus was rare in this study, even among those with frequent symptoms.
Associations between a priori-defined dietary patterns and longitudinal changes in bone mineral density in adolescents

Abstract Objective To quantify short- and long-term associations between dietary patterns defined a priori and bone mineral density (BMD) during adolescence. Design Dietary patterns were defined at 13 years old using a Mediterranean diet (MD) quality index, the Dietary Approaches to Stop Hypertension (DASH) diet index and the Oslo Health Study (OHS) dietary index. Linear regression coefficients were used to estimate associations between dietary patterns and forearm BMD at 13 and 17 years, measured by dual-energy X-ray absorptiometry. Setting Public and private schools of Porto, Portugal. Subjects The EPITeen cohort comprising 1180 adolescents born in 1990, recruited at schools during the 2003/2004 school year and re-evaluated in 2007/2008. Results In girls, at 13 years, mean BMD (g/cm2) in the first and third tertiles was 0·369 and 0·368 for the MD pattern, 0·368 and 0·369 for the DASH diet, and 0·370 and 0·363 for the OHS index. In boys, mean BMD (g/cm2) in the first and third tertiles was 0·338 and 0·347 for the MD pattern, 0·342 and 0·346 for the DASH diet, and 0·344 and 0·342 for the OHS index. None of these differences were significant. Mean BMD at 17 years and prospective variation were also not significantly different between tertiles of adherence to each score. However, a trend of increased BMD at 13 years with greater adherence to the MD pattern was observed in boys (adjusted coefficient = 0·248; 95 % CI 0·052, 0·444). Conclusions The selected dietary patterns may not capture truly important dietary differences in determining BMD or diet may not be, beyond nutrient adequacy, a limiting determinant of BMD.
Relationship of worksite smoking policy to changes in employee tobacco use: findings from COMMIT. Community Intervention Trial for Smoking Cessation.

OBJECTIVE: To report data on the impact of worksite smoking policies on employee smoking behaviour from a large and heterogeneous sample of smokers and worksites in 22 different communities across North America participating in the COMMIT trial. DESIGN AND SUBJECTS: Data from a population-based survey of 8271 employed adult smokers who completed surveys in 1988 and 1993. Surveys included questions on tobacco use behaviours, personal/demographic characteristics, and smoking policy and cessation resources at the workplace. RESULTS: After controlling for potential confounding factors, regression analyses revealed that employees who worked in a smoke-free worksite were over 25% more likely to make a serious quit attempt between 1988 and 1993, and over 25% more likely to achieve cessation than those who worked in a worksite that permitted smoking. Among continuing smokers, employees in smoke-free worksites consumed an average of 2 3/4 fewer cigarettes per day compared with those who worked in places with a non-restrictive smoking policy. A smoke-free worksite policy was not associated with a greater likelihood of using smokeless tobacco. CONCLUSION: These data, from one of the largest and longest smoking cessation studies to date, add support to the conclusion that smoke-free worksite policies help employees to reduce or discontinue use of tobacco.
The suprachiasmatic nucleus controls the daily variation of plasma glucose via the autonomic output to the liver: are the clock genes involved?

In order to drive tissue‐specific rhythmic outputs, the master clock, located in the suprachiasmatic nucleus (SCN), is thought to reset peripheral oscillators via either chemical and hormonal cues or neural connections. Recently, the daily rhythm of plasma glucose (characterized by a peak before the onset of the activity period) has been shown to be directly driven by the SCN, independently of the SCN control of rhythmic feeding behaviour. Indeed, the daily variation in glucose was not impaired unless the scheduled feeding regimen (six‐meal schedule) was associated with an SCN lesion. Here we show that the rhythmicity of both clock‐gene mRNA expression in the liver and plasma glucose is not abolished under such a regular feeding schedule. Because the onset of the activity period and hyperglycemia are correlated with an increased sympathetic tonus, we investigated whether this autonomic branch is involved in the SCN control of plasma glucose rhythm and liver rhythmicity. Interestingly, hepatic sympathectomy combined with a six‐meal feeding schedule resulted in a disruption of the plasma glucose rhythmicity without affecting the daily variation in clock‐gene mRNA expression in the liver. Taking all these data together, we conclude that (i) the SCN needs the sympathetic pathway to the liver to generate the 24‐h rhythm in plasma glucose concentrations, (ii) rhythmic clock‐gene expression in the liver is not dependent on the sympathetic liver innervation and (iii) clock‐gene rhythmicity in liver cells is not sufficient for sustaining a circadian rhythm in plasma glucose concentrations.
New antiepileptic drugs: a systematic review of their efficacy and tolerability

Abstract Objectives: To evaluate the efficacy and tolerability of the newly developed antiepileptic drugs gabapentin, lamotrigine, tiagabine, topiramate, vigabatrin, and zonisamide in patients with refractory partial epilepsy. Design: Systematic review of published and unpublished randomised controlled trials of add-on treatment with new antiepileptic drugs. Subjects: 20 published and eight unpublished trials representing 3883 patients with refractory partial epilepsy. Main outcome measures: Proportion of patients who (a) showed 50% or greater reduction in frequency of seizures (50% responders) and (b) withdrew from each study for any reason. Results: Odds ratios (95% confidence intervals) relative to placebo for 50% responders were 2.29 (1.53 to 3.43) for gabapentin, 2.32 (1.47 to 3.68) for lamotrigine, 3.03 (2.01 to 4.58) for tiagabine, 4.22 (2.80 to 6.35) for topiramate, 3.68 (2.45 to 5.51) for vigabatrin, and 2.47 (1.36 to 4.47) for zonisamide. Odds ratios for withdrawal were 1.36 (0.75 to 2.49) for gabapentin, 1.19 (0.79 to 1.79) for lamotrigine, 1.81 (1.21 to 2.70) for tiagabine, 2.42 (1.43 to 4.11) for topiramate, 2.58 (1.26 to 5.27) for vigabatrin, and 5.70 (1.76 to 18.49) for zonisamide. Comparing results for each drug showed that all of the 95% confidence intervals overlapped, indicating that they were not significantly different in terms of efficacy and tolerability. Conclusions: All six drugs were significantly better than placebo at reducing frequency of seizures. These results do not allow an evidence based choice between these drugs as we have no conclusive indication of differences in efficacy or tolerability. Key messages At present there is insufficient evidence to guide a choice between these new treatments We systematically reviewed randomised placebo controlled studies of supplementary gabapentin, lamotrigine, tiagabine, topiramate, vigabatrin, and zonisamide Each drug was significantly better than placebo at preventing seizures, but none was significantly different from the others in terms of efficacy or tolerability, though the confidence intervals were wide Randomised trials comparing active treatments are needed to further evaluate these drugs
An automated web surface inspection for hot wire rod using undecimated wavelet transform and support vector machine

This paper presents defect detection and classification method for hot wire rod in the steel industry. The detection algorithm is based on undecimated discrete wavelet transform (UDWT). The algorithm utilizes the translation invariant property of UDWT. To discriminate the real defects and pseudo defects, we use support vector machine (SVM). The total 14 feature attributes are extracted from binary and gray image. To select best model for SVM classier, we search the parameter spaces by exponentially growing sampling test. The experimental results show the proposed methods can be applied to real-world application.