LLukas22/scidocs huggingface dataset:
Immune reconstitution and outcome after unrelated cord blood transplantation: a single paediatric institution experience

We report the outcome of 12 children who underwent unrelated cord blood transplant (U-CBT) in a single institution between February 1997 and July 1998. The 1 year event-free survival was 67% (95% CI of 26%). Four children died with infectious complication as cause of death in three cases. Immune reconstitution was studied during first year post transplant by assaying total lymphocyte counts, B cells, NK cells and T cell subsets in the eight disease-free surviving patients. We observed a prompt recovery of CD19+ cell number which was greater than 500/μl at 9 months for all patients except the one with severe cGVHD. B cells constituted the predominant lymphocyte subset at 6 and 9 months post transplant with normal or elevated B cell numbers according to normal paediatric range. We noted normal serum immunoglobulin levels at 6 months post transplant for IgA and IgM and at 9 months for IgG. The CD3+ cell count and particularly the CD3+CD8+ T cell subset remained depressed until 12 months post transplant. Six months after unrelated CBT, seven out of eight patients had less than 100 CD3+CD8+ cells/μl. CD3+CD4+ cell recovery was less impaired with all children achieving an absolute count of CD3+CD4+ cells greater than 200/μl during the first year in a median of 5 months. The percentage of NK cells was elevated during the first 6 months after CBT but their absolute count remained within the normal range. Bone Marrow Transplantation (2000) 25, 53–57.
Does physiotherapy reduce the incidence of postoperative complications in patients following pulmonary resection via thoracotomy? a protocol for a randomised controlled trial

BACKGROUND
Postoperative pulmonary and shoulder complications are important causes of postoperative morbidity following thoracotomy. While physiotherapy aims to prevent or minimise these complications, currently there are no randomised controlled trials to support or refute effectiveness of physiotherapy in this setting.


METHODS/DESIGN
This single blind randomised controlled trial aims to recruit 184 patients following lung resection via open thoracotomy. All subjects will receive a preoperative physiotherapy information booklet and following surgery will be randomly allocated to a Treatment Group receiving postoperative physiotherapy or a Control Group receiving standard care nursing and medical interventions but no physiotherapy. The Treatment Group will receive a standardised daily physiotherapy programme to prevent respiratory and musculoskeletal complications. On discharge Treatment Group subjects will receive an exercise programme and exercise diary to complete. The primary outcome measure is the incidence of postoperative pulmonary complications, which will be determined on a daily basis whilst the patient is in hospital by a blinded assessor. Secondary outcome measures are the length of postoperative hospital stay, severity of pain, shoulder function as measured by the self-reported shoulder pain and disability index, and quality of life measured by the Medical Outcomes Study Short Form 36 v2 New Zealand standard version. Pain, shoulder function and quality of life will be measured at baseline, on discharge from hospital, one month and three months postoperatively. Additionally a subgroup of subjects will have measurement of shoulder range of movement and muscle strength by a blinded assessor.


DISCUSSION
Results from this study will contribute to the increasing volume of evidence regarding the effectiveness of physiotherapy following major surgery and will guide physiotherapists in their interventions for patients following thoracotomy.


TRIAL REGISTRATION
The study protocol is registered with the Australian and New Zealand Clinical Trials registry (ANZCTRN12605000201673).
Randomized trial of clazosentan in patients with aneurysmal subarachnoid hemorrhage undergoing endovascular coiling.

BACKGROUND AND PURPOSE
Clazosentan, an endothelin receptor antagonist, has been shown to reduce vasospasm after aneurysmal subarachnoid hemorrhage (aSAH). CONSCIOUS-3 assessed whether clazosentan reduced vasospasm-related morbidity and all-cause mortality postaSAH secured by endovascular coiling.


METHODS
This double-blind, placebo-controlled, phase III trial randomized patients with aSAH secured by endovascular coiling to ≤ 14 days intravenous clazosentan (5 or 15 mg/h) or placebo. The primary composite end point (all-cause mortality; vasospasm-related new cerebral infarcts or delayed ischemic neurological deficits; rescue therapy for vasospasm) was evaluated 6 weeks postaSAH. The main secondary end point was dichotomized extended Glasgow Outcome Scale (week 12).


RESULTS
CONSCIOUS-3 was halted prematurely following completion of CONSCIOUS-2; 577/1500 of planned patients (38%) were enrolled and 571 were treated (placebo, n=189; clazosentan 5 mg/h, n=194; clazosentan 15 mg/h, n=188). The primary end point occurred in 50/189 of placebo-treated patients (27%), compared with 47/194 patients (24%) treated with clazosentan 5 mg/h (odds ratio [OR], 0.786; 95% CI, 0.479-1.289; P=0.340), and 28/188 patients (15%) treated with clazosentan 15 mg/h (OR, 0.474; 95% CI, 0.275-0.818; P=0.007). Poor outcome (extended Glasgow Outcome Scale score ≤ 4) occurred in 24% of patients with placebo, 25% of patients with clazosentan 5 mg/h (OR, 0.918; 95% CI, 0.546-1.544; P=0.748), and 28% of patients with clazosentan 15 mg/h (OR, 1.337; 95% CI, 0.802-2.227; P=0.266). Pulmonary complications, anemia, and hypotension were more common in patients who received clazosentan than in those who received placebo. At week 12, mortality was 6%, 4%, and 6% with placebo, clazosentan 5 mg/h, and clazosentan 15 mg/h, respectively.


CONCLUSIONS
Clazosentan 15 mg/h significantly reduced postaSAH vasospasm-related morbidity/all-cause mortality; however, neither dose improved outcome (extended Glasgow Outcome Scale).
Considering Cost Asymmetry in Learning Classifiers

Receiver Operating Characteristic (ROC) curves are a standard way to display the performance of a set of binary classifiers for all feasible ratios of the costs associated with false positives and false negatives. For linear classifiers, the set of classifiers is typically obtained by training once, holding constant the estimated slope and then varying the intercept to obtain a parameterized set of classifiers whose performances can be plotted in the ROC plane. We consider the alternative of varying the asymmetry of the cost function used for training. We show that the ROC curve obtained by varying both the intercept and the asymmetry, and hence the slope, always outperforms the ROC curve obtained by varying only the intercept. In addition, we present a path-following algorithm for the support vector machine (SVM) that can compute efficiently the entire ROC curve, and that has the same computational complexity as training a single classifier. Finally, we provide a theoretical analysis of the relationship between the asymmetric cost model assumed when training a classifier and the cost model assumed in applying the classifier. In particular, we show that the mismatch between the step function used for testing and its convex upper bounds, usually used for training, leads to a provable and quantifiable difference around extreme asymmetries.
: Past , Present , Future

We thank Steve Burks, Dick Thaler, and especially Matthew Rabin (who collaborated during part of the process) for helpful comments.
The Abell cluster A586 and the detection of violation of the equivalence principle

We discuss the current bounds on the Equivalence Principle (EP), in particular from structure formation and, reexamine in this context, the recent claim on the evidence of the interaction between dark matter and dark energy in the Abell Cluster A586 and the ensued violation of the EP.
Effects of wave-current interaction on rip currents

[1] The time evolution of rip currents in the nearshore is studied by numerical experiments. The generation of rip currents is due to waves propagating and breaking over alongshore variable topography. Our main focus is to examine the significance of wave-current interaction as it affects the subsequent development of the currents, in particular when the currents are weak compared to the wave speed. We describe the dynamics of currents using the shallow water equations with linear bottom friction and wave forcing parameterized utilizing the radiation stress concept. The slow variations of the wave field, in terms of local wave number, frequency, and energy (wave amplitude), are described using the ray theory with the inclusion of energy dissipation due to breaking. The results show that the offshore directed rip currents interact with the incident waves to produce a negative feedback on the wave forcing, hence to reduce the strength and offshore extent of the currents. In particular, this feedback effect supersedes the bottom friction such that the circulation patterns become less sensitive to a change of the bottom friction parameterization. The two physical processes arising from refraction by currents, bending of wave rays and changes of wave energy, are both found to be important. The onset of instabilities of circulations occurs at the nearshore region where rips are ‘‘fed,’’ rather than offshore at rip heads as predicted with no wave-current interaction. The unsteady flows are characterized by vortex shedding, pairing, and offshore migration. Instabilities are sensitive to the angle of wave incidence and the spacing of rip channels.
A Large Dataset for Improving Patch Matching

We propose a new dataset for learning local image descriptors which can be used for significantly improved patch matching. Our proposed dataset consists of an order of magnitude more number of scenes, images, and positive and negative correspondences compared to the currently available Multi-View Stereo (MVS) dataset from Brown et al. [1]. The new dataset also has better coverage of the overall viewpoint, scale, and lighting changes in comparison to the MVS dataset. Our dataset also provides supplementary information like RGB patches with scale and rotations values, and intrinsic and extrinsic camera parameters which as shown later can be used to customize training data as per application. We train an existing state-of-the-art model on our dataset and evaluate on publicly available benchmarks such as HPatches dataset [2] and Strecha et al. [3] to quantify the image descriptor performance. Experimental evaluations show that the descriptors trained using our proposed dataset outperform the current state-of-the-art descriptors trained on MVS by 8%, 4% and 10% on matching, verification and retrieval tasks respectively on the HPatches dataset. Similarly on the Strecha dataset, we see an improvement of 3-5% for the matching task in non-planar scenes.
Adaptive Algorithms for Acoustic Echo Cancellation: A Review

One of the major issues involved with communication is acoustic echo, which is actually a delayed version of sound reflected back to the source of sound hampering communication. Cancellation of these involve the use of acoustic echo cancellers involving adaptive filters governed by adaptive algorithms. This paper presents a review of some of the algorithms of acoustic echo cancellation covering their merits and demerits. Various algorithms like LMS, NLMS, FLMS, LLMS, RLS, AFA, LMF have been discussed. Keywords— Adaptive Filter, Acoustic Echo, LMS, NLMS, FX-LMS, AAF, LLMS, RLS.
Improved Subset Autoregression: With R Package

The FitAR R (R Development Core Team 2008) package that is available on the Comprehensive R Archive Network is described. This package provides a comprehensive approach to fitting autoregressive and subset autoregressive time series. For long time series with complicated autocorrelation behavior, such as the monthly sunspot numbers, subset autoregression may prove more feasible and/or parsimonious than using AR or ARMA models. The two principal functions in this package are SelectModel and FitAR for automatic model selection and model fitting respectively. In addition to the regular autoregressive model and the usual subset autoregressive models (Tong 1977), these functions implement a new family of models. This new family of subset autoregressive models is obtained by using the partial autocorrelations as parameters and then selecting a subset of these parameters. Further properties and results for these models are discussed in McLeod and Zhang (2006). The advantages of this approach are that not only is an efficient algorithm for exact maximum likelihood implemented but that efficient methods are derived for selecting high-order subset models that may occur in massive datasets containing long time series. A new improved extended BIC criterion, UBIC, developed by Chen and Chen (2008) is implemented for subset model selection. A complete suite of model building functions for each of the three types of autoregressive models described above are included in the package. The package includes functions for time series plots, diagnostic testing and plotting, bootstrapping, simulation, forecasting, Box-Cox analysis, spectral density estimation and other useful time series procedures. As well as methods for standard generic functions including print, plot, predict and others, some new generic functions and methods are supplied that make it easier to work with the output from FitAR for bootstrapping, simulation, spectral density estimation and Box-Cox analysis.
PCB pollution continues to impact populations of orcas and other dolphins in European waters

Organochlorine (OC) pesticides and the more persistent polychlorinated biphenyls (PCBs) have well-established dose-dependent toxicities to birds, fish and mammals in experimental studies, but the actual impact of OC pollutants on European marine top predators remains unknown. Here we show that several cetacean species have very high mean blubber PCB concentrations likely to cause population declines and suppress population recovery. In a large pan-European meta-analysis of stranded (n = 929) or biopsied (n = 152) cetaceans, three out of four species:- striped dolphins (SDs), bottlenose dolphins (BNDs) and killer whales (KWs) had mean PCB levels that markedly exceeded all known marine mammal PCB toxicity thresholds. Some locations (e.g. western Mediterranean Sea, south-west Iberian Peninsula) are global PCB "hotspots" for marine mammals. Blubber PCB concentrations initially declined following a mid-1980s EU ban, but have since stabilised in UK harbour porpoises and SDs in the western Mediterranean Sea. Some small or declining populations of BNDs and KWs in the NE Atlantic were associated with low recruitment, consistent with PCB-induced reproductive toxicity. Despite regulations and mitigation measures to reduce PCB pollution, their biomagnification in marine food webs continues to cause severe impacts among cetacean top predators in European seas.
Multi-space Variational Encoder-Decoders for Semi-supervised Labeled Sequence Transduction

Labeled sequence transduction is a task of transforming one sequence into another sequence that satisfies desiderata specified by a set of labels. In this paper we propose multi-space variational encoderdecoders, a new model for labeled sequence transduction with semi-supervised learning. The generative model can use neural networks to handle both discrete and continuous latent variables to exploit various features of data. Experiments show that our model provides not only a powerful supervised framework but also can effectively take advantage of the unlabeled data. On the SIGMORPHON morphological inflection benchmark, our model outperforms single-model state-ofart results by a large margin for the majority of languages.1
A process for systematically reviewing the literature: providing the research evidence for public health nursing interventions.

BACKGROUND
Several groups have outlined methodologies for systematic literature reviews of the effectiveness of interventions. The Effective Public Health Practice Project (EPHPP) began in 1998. Its mandate is to provide research evidence to guide and support the Ontario Ministry of Health in outlining minimum requirements for public health services in the province. Also, the project is expected to disseminate the results provincially, nationally, and internationally. Most of the reviews are relevant to public health nursing practice.


AIMS
This article describes four issues related to the systematic literature reviews of the effectiveness of public health nursing interventions: (1) the process of systematically reviewing the literature, (2) the development of a quality assessment instrument, (3) the results of the EPHPP to date, and (4) some results of the dissemination strategies used.


METHODS
The eight steps of the systematic review process including question formulation, searching and retrieving the literature, establishing relevance criteria, assessing studies for relevance, assessing relevant studies for methodological quality, data extraction and synthesis, writing the report, and dissemination are outlined. Also, the development and assessment of content and construct validity and intrarater reliability of the quality assessment questionnaire used in the process are described.


RESULTS
More than 20 systematic reviews have been completed. Content validity was ascertained by the use of a number of experts to review the questionnaire during its development. Construct validity was demonstrated through comparisons with another highly rated instrument. Intrarater reliability was established using Cohen's Kappa. Dissemination strategies used appear to be effective in that professionals report being aware of the reviews and using them in program planning/policymaking decisions.


CONCLUSIONS
The EPHPP has demonstrated the ability to adapt the most current methods of systematic literature reviews of effectiveness to questions related to public health nursing. Other positive outcomes from the process include the development of a critical mass of public health researchers and practitioners who can actively participate in the process, and the work on dissemination has been successful in attracting external funds. A program of research in this area is being developed.
Plant defense, herbivory, and the growth of Cordia alliodora trees and their symbiotic Azteca ant colonies

The effects of herbivory on plant fitness are integrated over a plant’s lifetime, mediated by ontogenetic changes in plant defense, tolerance, and herbivore pressure. In symbiotic ant–plant mutualisms, plants provide nesting space and food for ants, and ants defend plants against herbivores. The benefit to the plant of sustaining the growth of symbiotic ant colonies depends on whether defense by the growing ant colony outpaces the plant’s growth in defendable area and associated herbivore pressure. These relationships were investigated in the symbiotic mutualism between Cordia alliodora trees and Azteca pittieri ants in a Mexican tropical dry forest. As ant colonies grew, worker production remained constant relative to ant-colony size. As trees grew, leaf production increased relative to tree size. Moreover, larger trees hosted lower densities of ants, suggesting that ant-colony growth did not keep pace with tree growth. On leaves with ants experimentally excluded, herbivory per unit leaf area increased exponentially with tree size, indicating that larger trees experienced higher herbivore pressure per leaf area than smaller trees. Even with ant defense, herbivory increased with tree size. Therefore, although larger trees had larger ant colonies, ant density was lower in larger trees, and the ant colonies did not provide sufficient defense to compensate for the higher herbivore pressure in larger trees. These results suggest that in this system the tree can decrease herbivory by promoting ant-colony growth, i.e., sustaining space and food investment in ants, as long as the tree continues to grow.
Radioiodine therapy dosimetry in benign thyroid disease and differentiated thyroid carcinoma

Traditionally, nuclear medicine has been regarded mainly as a diagnostic specialty in which the administration of radioactive substances yields information whose importance far outweighs any potential risk to normal tissue. Now, however, therapeutic applications of radionuclide-based approaches are at last gaining the prominence they deserve. In this field, individual patient dosimetry is essential both for optimising the administered activity through the establishment of minimum effective and maximum tolerated absorbed doses and for determining a dose-response relationship as a basis for predicting tumour response [2]. Unfortunately, the lack of comprehensive clinical trials designed to bring out the value of radionuclide dosimetry in predicting therapy outcome has fed a general belief that dosimetry methods are daunting, prone to a large degree of uncertainty, and liable to generate increased costs, and thus held back their progress. This is, indeed, why Flux and colleagues remarked “radionuclide therapy remains the Cinderella of cancer treatment modalities, under-utilised with respect to more conventional treatments” [3]. Now, however, the availability of new technologies (e.g. PET/CT) and radioisotope pairs for diagnosis and therapy (e.g. I and I or Y and Y), supported by a new generation of personal computer software for internal dose assessment, is at last leading to an increase in the use of dosimetry in clinical therapeutic applications. To show the appreciable progress now being made in this field we here take a look at a sample of the most recent literature on dosimetry for radioiodine treatment of benign thyroid disease and differentiated thyroid carcinoma.
A novel hysteresis bandwidth (NHB) calculation to fix the switching frequency employed in active power filter

Variable switching process is the main issue in practical implementation of fixed band hysteresis current controller in active power filters (APF) that increases the switching frequency and switching losses in power systems. Preventing this case, the Adaptive Hysteresis Current Control (AHCC) has been introduced and developed by many researchers. By this way, The Hysteresis Band (HB) will change adaptively by system parameters in order to control the switching speed and fix the switching frequency. In this paper a revisory method for the hysteresis bandwidth calculation procedure is proposed that makes switching frequency invariable significantly. The APF Simulations using proposed method (NHB) in Matlab/Simulink environment has been done. Results including switching frequency and current source TDH have been given to prove the efficiency of this method.
The effect of the field of constants on the number of multiplications

New algorithms for computing the Discrete Fourier Transform of n points are described. For n in the range of a few tens to a few thousands these algorithms use substantially fewer multiplications than the best algorithm previously known, and about the same number of additions.