LLukas22/scidocs huggingface dataset:
Analysis of Half-Quadratic Minimization Methods for Signal and Image Recovery

We address the minimization of regularized convex cost functions which are customarily used for edge-preserving restoration and reconstruction of signals and images. In order to accelerate computation, the multiplicative and the additive half-quadratic reformulation of the original cost-function have been pioneered in Geman and Reynolds [IEEE Trans. Pattern Anal. Machine Intelligence, 14 (1992), pp. 367–383] and Geman and Yang [IEEE Trans. Image Process., 4 (1995), pp. 932–946]. The alternate minimization of the resultant (augmented) cost-functions has a simple explicit form. The goal of this paper is to provide a systematic analysis of the convergence rate achieved by these methods. For the multiplicative and additive half-quadratic regularizations, we determine their upper bounds for their root-convergence factors. The bound for the multiplicative form is seen to be always smaller than the bound for the additive form. Experiments show that the number of iterations required for convergence for the multiplicative form is always less than that for the additive form. However, the computational cost of each iteration is much higher for the multiplicative form than for the additive form. The global assessment is that minimization using the additive form of half-quadratic regularization is faster than using the multiplicative form. When the additive form is applicable, it is hence recommended. Extensive experiments demonstrate that in our MATLAB implementation, both methods are substantially faster (in terms of computational times) than the standard MATLAB Optimization Toolbox routines used in our comparison study.
Rapid inpatient/outpatient desensitization for chemotherapy hypersensitivity: standard protocol effective in 57 patients for 255 courses.

OBJECTIVES
Hypersensitivity reactions (HR) to chemotherapy often prompt permanent discontinuation and deprive the patient of the most active regimen. We investigated the safety and effectiveness of a rapid desensitization protocol used in inpatient and outpatient settings for patients with HR to various chemotherapy and related agents.


METHODS
A 3-solution, 12-step protocol delivered doubling drug doses by step, infusing the target dose over 5.8 h for inpatient and 3.8 h for outpatient administration.


RESULTS
57 consecutive patients who had moderate to severe HR to chemotherapy were evaluated for desensitization. All 57 patients successfully completed 255 courses of desensitization (127 to carboplatin, 114 to paclitaxel, and 14 to four other agents) where 16 patients received 51 courses in the outpatient setting (34 to carboplatin and 17 to paclitaxel). 225 courses (88.2%) were completed without any HR. 18 patients had breakthrough symptoms (BS) over 30 courses (11.8%) that were less severe than their initial HR. After management of breakthrough symptoms, these patients finished all 30 courses and tolerated subsequent desensitizations on a modified protocol. 21 of 26 patients (81%) with HR to carboplatin had positive skin tests to carboplatin. Cancer response to chemotherapy administered by desensitization was within the expected range after 1-3 years of follow-up.


CONCLUSION
The rapid desensitization protocol was safe and effective in both the inpatient and outpatient settings and allowed appropriate patients with moderate to severe HR to continue chemotherapy. This study warrants the incorporation of the protocol into standard clinical practice.
Antiviral activity and tolerability of amdoxovir with zidovudine in a randomized double-blind placebo-controlled study in HIV-1-infected individuals.

BACKGROUND
Amdoxovir acts synergistically with zidovudine in vitro and the combination prevents or delays the selection of thymidine analogue and K65R mutations. In silico studies have shown that a reduced dose of zidovudine (200 mg) results in decreased zidovudine-monophosphate levels, associated with toxicity, while maintaining zidovudine-triphosphate levels, which are associated with antiviral effects. Here, we aimed to assess the short-term tolerability and antiviral activity of amdoxovir in combination with reduced and standard doses of zidovudine.


METHODS
The study was a double-blind, placebo-controlled study in HIV-1-infected patients not receiving antiretroviral therapy and with plasma HIV-1 RNA > or =5,000 copies/ml. Patients were randomized to 10 days of twice-daily treatment with 200 mg zidovudine, 300 mg zidovudine, 500 mg amdoxovir, 500 mg amdoxovir plus 200 mg zidovudine or 500 mg amdoxovir plus 300 mg zidovudine. The mean change in viral load (VL) log(10) and area under the virus depletion curve (AUC(VL)) from baseline to day 10 were determined. Laboratory and clinical safety monitoring were performed.


RESULTS
Twenty-four patients were enrolled. The mean VL log(10) change was 0.10 with placebo, -0.69 with zidovudine 200 mg, -0.55 with zidovudine 300 mg, -1.09 with amdoxovir, -2.00 with amdoxovir plus zidovudine (200 mg) and -1.69 with amdoxovir plus zidovudine (300 mg). Amdoxovir plus zidovudine (200 mg) was significantly more potent than amdoxovir monotherapy in AUC(VL) and mean VL decline (P=0.019 and P=0.021, respectively), suggesting synergy. There was markedly decreased VL variability with the combination compared with amdoxovir alone. All adverse events were mild to moderate.


CONCLUSION
The combination of amdoxovir plus zidovudine appeared synergistic with reduced VL variability. This combined therapy, including the use of a lower zidovudine dosage, warrants further development for the therapy of HIV infection.
Ground States of σ‐Bonded Molecules. V. MINDO Treatment of Organic Compounds Containing Nitrogen or Oxygen

The MINDO approximation, described in Paper IV, has been extended to compounds containing nitrogen and oxygen. With assumed molecular geometries, the method gives very satisfactory estimates of heats of formation and dipole moments.
Crop Residue Removal for Bioenergy Reduces Soil Carbon Pools: How Can We Offset Carbon Losses?

Crop residue removal for bioenergy can deplete soil organic carbon (SOC) pools. Management strategies to counteract the adverse effects of residue removal on SOC pools have not been, however, widely discussed. This paper reviews potential practices that can be used to offset the SOC lost with residue removal. Literature indicates that practices including no-till cover crops, manure and compost application, and return of biofuel co-products increase SOC pools and may thus be used to offset some SOC loss. No-till rotations that include semi-perennial grasses or legumes also offer a promise to promote soil-profile C sequestration and improve soil resilience after residue removal. No-till cover crops can sequester between 0.10 and 1 Mg ha−1 per year of SOC relative to no-till without cover crops, depending on cover crop species, soil type, and precipitation input. Animal manure and compost contain about 15 % of C and thus their addition to soil can enhance SOC pools and boost soil biological activity. Similarly, application of biofuel co-products such as biochar, which contain between 45 % and 85 % of C depending on the feedstock source and processing method, can enhance long-term C sequestration. These mitigation strategies may maintain SOC pools under partial residue removal in no-till soils but are unlikely to replace all the SOC lost if residue is removed at excessive rates. More field research and modeling efforts are needed to assess the magnitude at which the different mitigation strategies can overcome SOC loss with crop residue removal.
Genetic mapping of QTLs affecting productivity and plant architecture in a full-sib cross from non-inbred parents in Cassava (Manihot esculenta Crantz)

An attempt was made to identify quantitative trait loci (QTLs) for several productivity and plant architecture traits in a full-sib progeny of 144 individuals from two non-inbred parents in cassava. A molecular linkage map of this cross constructed previously with over 250 markers was the source of molecular markers. The progeny were grown under field conditions at two locations (Palmira and Quilichao) in Colombia and evaluated in 2 years (1998 and 1999) for architecture and productivity traits. Architecture traits evaluated were plant height (PH), branching height (BH), branching levels (BL), branching index (BI), stem portion with leaves (SPL) and leaf area index (LAI). Productivity traits were those related to total dry matter production and distribution, namely fresh root yield (FRY), fresh shoot yield (FSY), harvest index (HI) and the number of storage roots (NR). Phenotypic evaluation of the traits in this population revealed continuous variation for all traits. Broad-sense heritability estimates, ranged from 36% (for NR) to 94% (for BH). Several significant phenotypic correlations were observed between architecture and productivity traits. Primary QTLs, using the single-QTL model, and secondary QTLs, by a primary QTL interaction model, were detected by interval mapping. A total of 30 primary QTLs and 84 secondary QTLs were detected. We identified 35% of detected QTLs in two or more trials, the other QTLs were environment-specific. These results underscore the significant genotype × environment interactions found for most of the traits. Several genomic segments affecting multiple traits were identified and were in agreement with correlation among traits. All QTLs identified for FRY were found associated with either component traits of productivity or architecture traits. This study suggests that QTLs for plant architecture can be used to improve productivity. However an exhaustive search and analysis of QTLs controlling architecture is required before marker-assisted selection (MAS) for increasing productivity can be initiated.
Fistulizing Crohn's Disease Presenting After Surgery on a Perianal Lesion.

Perianal skin lesions, such as skin tags, can be an early presenting sign of Crohn's disease. Surgical intervention on these lesions may increase the risk of fistula development and lead to worse outcomes. This case series examined 8 patients who underwent surgical intervention on what appeared to be benign perianal skin lesions, only to reveal fistulas leading to the diagnosis of Crohn's disease. This patient population comprised 20% of all pediatric patients with Crohn's disease who had perianal fistula present at diagnosis. The initial type of perianal lesion varied from case to case and included skin tags, hemorrhoids, and perianal abscesses. All of the patients had other presenting features that, in retrospect, may have been attributed to Crohn's disease. None presented solely with a perianal lesion. Four patients had weight loss or growth failure. Most of the remainder had abnormal laboratory test results. These findings should raise the awareness of primary care providers that perianal lesions can be the first presenting sign of possible Crohn's disease in otherwise healthy appearing children. Such children should undergo a thorough evaluation for Crohn's disease before surgical intervention on perianal lesions because surgical procedures may be associated with worse outcomes.
Triangle Generative Adversarial Networks

A Triangle Generative Adversarial Network (∆-GAN) is developed for semisupervised cross-domain joint distribution matching, where the training data consists of samples from each domain, and supervision of domain correspondence is provided by only a few paired samples. ∆-GAN consists of four neural networks, two generators and two discriminators. The generators are designed to learn the two-way conditional distributions between the two domains, while the discriminators implicitly define a ternary discriminative function, which is trained to distinguish real data pairs and two kinds of fake data pairs. The generators and discriminators are trained together using adversarial learning. Under mild assumptions, in theory the joint distributions characterized by the two generators concentrate to the data distribution. In experiments, three different kinds of domain pairs are considered, image-label, image-image and image-attribute pairs. Experiments on semi-supervised image classification, image-to-image translation and attribute-based image generation demonstrate the superiority of the proposed approach.
Effects of paroxetine on the pharmacokinetics and pharmacodynamics of immediate-release and extended-release metoprolol.

STUDY OBJECTIVE
To compare the effects of paroxetine on the pharmacokinetics and pharmacodynamics of the immediate-release (IR) and extended-release (ER) formulations of metoprolol.


DESIGN
Prospective, randomized, open-label, 3-way crossover study.


SETTING
General clinical research center.


SUBJECTS
Fifteen healthy volunteers with at least one active cytochrome P450 (CYP) CYP2D6 allele (CYP2D6*1 or CYP2D6*2).


INTERVENTION
In each of three phases conducted in random sequence, subjects received one of three metoprolol formulations administered on day 1: a single dose of metoprolol ER 100 mg, a single dose of metoprolol ER 200 mg, or two 100-mg doses of metoprolol IR administered 12 hours apart. Oral paroxetine 20 mg/day was then given alone on days 2-7 and coadministered with the same metoprolol formulation on day 8. Subjects received each of the other two formulations during the next two phases, with a 14-day washout period between each phase.


MEASUREMENTS AND MAIN RESULTS
After receiving metoprolol on days 1 (before paroxetine) and 8 (after paroxetine), S- and R-metoprolol pharmacokinetic parameters and exercise heart rate and blood pressure responses were measured. The mean area under the plasma concentration-time curve values of both S- and R-metoprolol for each formulation were increased approximately 3- and 4-fold, respectively, by paroxetine. Paroxetine significantly increased the S- and R-metoprolol maximum concentration (C(max)) of each formulation and increased the elimination half-life of both isomers approximately 2-fold. When metoprolol IR was given with paroxetine, the S-metoprolol C(max) was significantly greater than that of either the 100-mg or 200-mg ER products. The maximum effect of metoprolol IR on heart rate was significantly greater than that of metoprolol ER 200 mg, independent of whether the agents were administered alone or with paroxetine. Both the heart rate and systolic blood pressure area under the effect-time curve values were significantly decreased by paroxetine.


CONCLUSION
Paroxetine significantly inhibits the metabolism of both metoprolol IR and ER, resulting in an increase in the magnitude and duration of [H9252]-blockade. The potential risk of adverse effects from excessive β-blockade may be greater with metoprolol IR than with metoprolol ER because of the significantly higher peak S-metoprolol plasma concentrations achieved with the IR formulation. Thus, if paroxetine treatment is indicated in patients receiving metoprolol, use of the ER formulation may reduce the risk of adverse effects.
Short- and long-term neuroadrenergic effects of moderate dietary sodium restriction in essential hypertension.

BACKGROUND
In essential hypertension, marked restrictions in dietary sodium intake cause in the short-term period an increase in muscle sympathetic nerve traffic (MSNA) and a baroreflex impairment. The present study was set out to assess on a long-term basis the neuroadrenergic and reflex effects of moderate sodium restriction.


METHODS AND RESULTS
In 11 untreated mild to moderate essential hypertensive patients (age 42.0+/-2.6 years, mean+/-SEM), we measured beat-to-beat blood pressure (Finapres), heart rate (ECG), and MSNA (microneurography) at rest and during stepwise intravenous infusions of phenylephrine and nitroprusside. Measurements were performed at regular sodium intake, after 1 and 8 weeks of low-sodium diet (80 mmol NaCl/d), and repeated again at regular sodium intake. After 1 week, urinary sodium excretion was markedly reduced. This was accompanied by a slight blood pressure reduction, no heart rate change, and a significant increase in plasma renin activity, aldosterone, and MSNA (+23.0+/-4.6% P<0.05). Whereas baroreflex heart-rate control was unchanged, baroreflex modulation of MSNA was reduced by 46.8+/-5.1% (P<0.01). At the end of the 8-week low-sodium diet, the neurohumoral and baroreflex responses were similar to the ones observed after 1 week of the dietary intervention. All changes disappeared when regular sodium diet was restored.


CONCLUSIONS
Thus, a moderate dietary sodium restriction triggers a sympathetic activation and a baroreflex impairment. Maintenance of low-sodium diet for several weeks does not attenuate these adverse adrenergic and reflex effects.
Recognizing Contextual Polarity in Phrase-Level Sentiment Analysis

This paper presents a new approach to phrase-level sentiment analysis that first determines whether an expression is neutral or polar and then disambiguates the polarity of the polar expressions. With this approach, the system is able to automatically identify thecontextual polarityfor a large subset of sentiment expressions, achieving results that are significantly better than baseline.
A systematic review of the therapeutic interventions for heterotopic ossification after spinal cord injury

Study design:Systematic review.Objective:To conduct a systematic review of the effectiveness of interventions used to prevent and treat heterotopic ossification (HO) after spinal cord injury (SCI).Setting:St Joseph's Parkwood Hospital, London, Ontario, Canada.Methods:MEDLINE, CINAHL, EMBASE and PsycINFO databases were searched for articles addressing the treatment of HO after SCI. Studies were selected by two reviewers and were only included for analysis if at least 50% of the subjects had an SCI, there were at least three SCI subjects and if the study subjects participated in a treatment or intervention. Study quality was assessed by two independent reviewers using the Downs and Black evaluation tool for all studies, as well as the PEDro assessment scale for randomized control trials only. Levels of evidence were assigned using a modified Sackett scale.Results:A total of 13 studies met the inclusion criteria. The selected articles were divided into prevention or treatment of post-SCI HO. Nonsteroidal anti-inflammatory drugs (NSAIDs), warfarin, and pulse low-intensity electrogmagnetic field (PLIMF) therapy were reviewed as prophylactic measures. Bisphosphonates, radiotherapy and excision were reviewed as treatments of post-SCI HO.Conclusions:Pharmacological treatments of HO after SCI had the highest level of research evidence supporting their use. Of these, NSAIDs showed greatest efficacy in the prevention of HO when administered early after an SCI, whereas bisphosphonates were the intervention with strongest supportive evidence once HO had developed. Of the non-pharmacological interventions, PLIMF was supported by the highest level of evidence; however, more research is needed to fully understand its role.
Design of An anthropomorphic tendon-driven robotic finger

The flexor digitorum profundus, extensor digitorum communis and lumbrical muscle of the human hand play a significant role in the movement of the finger. The structure consisting of these muscles and tendons is important to consider an anthropomorphic tendon-driven finger. However, there are some problems to apply the structure found in humans to robotic fingers using mechanical elements. One of them is that the origin of the lumbrical muscle is not on any bones but on the tendon of the flexor digitorum profundus. Another is the non-constant length of the moment arm of the lateral band at the proximal interphalangeal (PIP) joint. We propose a design based on the kinematic model proposed by Leijnse et al. [1] considering the equalization of the joint torques. The proposed model can be easily realized by a structure consisting of actuators fixed to a base and a tendon-pulley system that maintains the function of those three muscle and their tendons.
Comparison of (18)F-FET and (18)F-FDG PET in brain tumors.

UNLABELLED
The purpose of this study was to compare the diagnostic value of positron emission tomography (PET) using [(18)F]-fluorodeoxyglucose ((18)F-FDG) and O-(2-[(18)F]fluoroethyl)-l-tyrosine ((18)F-FET) in patients with brain lesions suspicious of cerebral gliomas.


METHODS
Fifty-two patients with suspicion of cerebral glioma were included in this study. From 30 to 50 min after injection of 180 MBq (18)F-FET, a first PET scan ((18)F-FET scan) was performed. Thereafter, 240 MBq (18)F-FDG was injected and a second PET scan was acquired from 30 to 60 min after the second injection ((18)F-FET/(18)F-FDG scan). The cerebral accumulation of (18)F-FDG was calculated by decay corrected subtraction of the (18)F-FET scan from the (18)F-FET/(18)F-FDG scan. Tracer uptake was evaluated by visual scoring and by lesion-to-background (L/B) ratios. The imaging results were compared with the histological results and prognosis.


RESULTS
Histology revealed 24 low-grade gliomas (LGG) of World Health Organization (WHO) Grade II and 19 high-grade gliomas (HGG) of WHO Grade III or IV, as well as nine others, mainly benign histologies. The gliomas showed increased (18)F-FET uptake (>normal brain) in 86% and increased (18)F-FDG uptake (>white matter) in 35%. (18)F-FET PET provided diagnostically useful delineation of tumor extent while this was impractical with (18)F-FDG due to high tracer uptake in the gray matter. A local maximum in the tumor area for biopsy guidance could be identified with (18)F-FET in 76% and with (18)F-FDG in 28%. The L/B ratios showed significant differences between LGG and HGG for both tracers but considerable overlap so that reliable preoperative grading was not possible. A significant correlation of tracer uptake with overall survival was found with (18)F-FDG only. In some benign lesions like abscesses, increased uptake was observed for both tracers indicating a limited specificity of both techniques.


CONCLUSIONS
(18)F-FET PET is superior to (18)F-FDG for biopsy guidance and treatment planning of cerebral gliomas. The uptake of (18)F-FDG is associated with prognosis, but the predictive value is limited and a histological evaluation of tumor tissue remains necessary. Therefore, amino acids like (18)F-FET are the preferred PET tracers for the clinical management of cerebral gliomas.
Successful discrimination of protein interactions.

We present results from the prediction of protein complexes associated with the first Critical Assessment of PRediction of Interactions (CAPRI) experiment. Our algorithm, SmoothDock, comprises four steps: (1) we perform rigid body docking using the program DOT, keeping the top 20,000 structures as ranked by surface complementarity; (2) we rerank these structures according to a free energy estimate that includes both desolvation and electrostatics and retain the top 2000 complexes; (3) we cluster the filtered complexes using a pairwise root-mean-square deviation (RMSD) criterion; (4) the 25 largest clusters are subject to a smooth docking discrimination algorithm where van der Waals forces are taken into account. We predicted targets 1, 6, and 7 with RMSDs of 9.5, 2.4, and 2.6 A, respectively. More importantly, from the perspective of biological applications, our approach consistently ranked the correct model first (i.e., with highest confidence). For target 5 we identified the binding region but not the correct orientation. Although we were able to find reasonable clusters for all targets, low-affinity complexes (K(d) < nM) were harder to discriminate. For four of seven targets, the top models predicted by our automated procedure were among the best communitywide predictions.