LLukas22/scidocs huggingface dataset:
Machine Learning Methods for Histopathological Image Analysis

Abundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using machine learning techniques. However, digital pathological images and related tasks have some issues to be considered. In this mini-review, we introduce the application of digital pathological image analysis using machine learning algorithms, address some problems specific to such analysis, and propose possible solutions.
A hierarchical volumetric shadow algorithm for single scattering

Volumetric effects such as beams of light through participating media are an important component in the appearance of the natural world. Many such effects can be faithfully modeled by a single scattering medium. In the presence of shadows, rendering these effects can be prohibitively expensive: current algorithms are based on ray marching, i.e., integrating the illumination scattered towards the camera along each view ray, modulated by visibility to the light source at each sample. Visibility must be determined for each sample using shadow rays or shadow-map lookups. We observe that in a suitably chosen coordinate system, the visibility function has a regular structure that we can exploit for significant acceleration compared to brute force sampling. We propose an efficient algorithm based on partial sum trees for computing the scattering integrals in a single-scattering homogeneous medium. On a CPU, we achieve speedups of 17–120x over ray marching. CR Categories: I.3.7 [Computer Graphics]: Three-Dimensional Graphics and Realism—Shadowing
What's the Risk? A simple approach for estimating adjusted risk measures from nonlinear models including logistic regression.

OBJECTIVE
To develop and validate a general method (called regression risk analysis) to estimate adjusted risk measures from logistic and other nonlinear multiple regression models. We show how to estimate standard errors for these estimates. These measures could supplant various approximations (e.g., adjusted odds ratio [AOR]) that may diverge, especially when outcomes are common.


STUDY DESIGN
Regression risk analysis estimates were compared with internal standards as well as with Mantel-Haenszel estimates, Poisson and log-binomial regressions, and a widely used (but flawed) equation to calculate adjusted risk ratios (ARR) from AOR.


DATA COLLECTION
Data sets produced using Monte Carlo simulations.


PRINCIPAL FINDINGS
Regression risk analysis accurately estimates ARR and differences directly from multiple regression models, even when confounders are continuous, distributions are skewed, outcomes are common, and effect size is large. It is statistically sound and intuitive, and has properties favoring it over other methods in many cases.


CONCLUSIONS
Regression risk analysis should be the new standard for presenting findings from multiple regression analysis of dichotomous outcomes for cross-sectional, cohort, and population-based case-control studies, particularly when outcomes are common or effect size is large.
Brain protection during ascending aortic repair for Stanford type A acute aortic dissection surgery. Nationwide analysis in Japan.

BACKGROUND
The optimal brain protection strategy for use during acute type A aortic dissection surgery is controversial.


METHODS AND RESULTS
We reviewed the results for 2 different methods: antegrade cerebral perfusion (ACP) and retrograde cerebral perfusion (RCP), during ascending aortic repair for acute type A aortic dissection for the period between 2008 and 2012 nationwide. Cases involving root repair, arch vessel reconstruction and/or concomitant procedures were excluded. Using the Japan Adult Cardiovascular Surgery Database, a total of 4,128 patients (ACP, n=2,769; RCP, n=1,359; mean age, 69.1±11.8 years; male 41.9%) were identified. The overall operative mortality was 8.6%. Following propensity score matching, among 1,320 matched pairs, differences in baseline characteristics between the 2 patient groups diminished. Cardiac arrest time (ACP 116±36 vs. RCP102±38 min, P<0.001), perfusion time (192±54 vs. 174±53 min, P<0.001) and operative time (378±117 vs. 340±108 min, P<0.001) were significantly shorter in the RCP group. There were no significant differences between the 2 groups regarding the incidence of operative mortality or neurological complications, including stroke (ACP 11.2% vs. RCP 9.7%). Postoperative ventilation time was significantly longer in the ACP group (ACP 128.9±355.7 vs. RCP 98.5±301.7 h, P=0.018). There were no differences in other early postoperative complications, such as re-exploration, renal failure, and mediastinitis.


CONCLUSIONS
Among patients undergoing dissection repair without arch vessel reconstruction, RCP had similar mortality and neurological outcome to ACP.
Effect of using ultrapure dialysate for hemodialysis on the level of circulating bacterial fragment in renal failure patients.

BACKGROUND
Cardiovascular disease is the major cause of mortality and morbidity in dialysis patients. Recently, circulating endotoxin is found to associate with the systemic inflammatory state and cardiovascular disease of dialysis patients. Previous studies showed that the use of ultrapure dialysate for hemodialysis could reduce the exposure to exogenous endotoxin. We studied the effect of using ultrapure dialysate for hemodialysis on circulating endotoxin and bacterial DNA fragment levels and vascular stiffness.


METHODS
This is an open-labeled prospective study of 25 patients (14 male). Circulating endotoxin and bacterial DNA level, vascular stiffness as represented by arterial pulse wave velocity (PWV), nutrition and hydration status were monitored before and repeatedly throughout 12 months after the use of ultrapure dialysate for hemodialysis.


RESULTS
The average age was 58.9 ± 10.2 years; 21 patients completed the study. Within 4 weeks of conversion to ultrapure dialysate for hemodialysis, the plasma endotoxin level fell from 0.302 ± 0.083 to 0.209 ± 0.044 EU/ml (p < 0.0001) and then remained static, while serum bacterial DNA level remained similar. Furthermore, the time-averaged plasma endotoxin level during the study period significantly correlated with serum C-reactive protein level (r = 0.483, p = 0.017), carotid-femoral PWV (r = 0.455, p = 0.033), and malnutrition inflammation score (r = 0.461, p = 0.031). The time-averaged serum bacterial DNA level significantly correlated with malnutrition inflammation score (r = 0.550, p = 0.008) and inversely with subjective global assessment score (r = -0.543, p = 0.009), but not with PWV.


CONCLUSIONS
In hemodialysis patients, circulating endotoxin level is associated with vascular stiffness and systemic inflammation. Using ultrapure dialysate for hemodialysis effectively reduces circulating endotoxin level in hemodialysis patients. The long-term benefit of using ultrapure dialysate for hemodialysis requires further study.
Chapter 12 DATA MINING IN SOCIAL MEDIA

The rise of online social media is providing a wealth of social network data. Data mining techniques provide researchers and practitioners the tools needed to analyze large, complex, and frequently changing social media data. This chapter introduces the basics of data mining, reviews social media, discusses how to mine social media data, and highlights some illustrative examples with an emphasis on social networking sites and blogs.
Sterilization of Allograft Bone: is 25 kGy the Gold Standard for Gamma Irradiation?

For several decades, a dose of 25 kGy of gamma irradiation has been recommended for terminal sterilization of medical products, including bone allografts. Practically, the application of a given gamma dose varies from tissue bank to tissue bank. While many banks use 25 kGy, some have adopted a higher dose, while some choose lower doses, and others do not use irradiation for terminal sterilization. A revolution in quality control in the tissue banking industry has occurred in line with development of quality assurance standards. These have resulted in significant reductions in the risk of contamination by microorganisms of final graft products. In light of these developments, there is sufficient rationale to re-establish a new standard dose, sufficient enough to sterilize allograft bone, while minimizing the adverse effects of gamma radiation on tissue properties. Using valid modifications, several authors have applied ISO standards to establish a radiation dose for bone allografts that is specific to systems employed in bone banking. These standards, and their verification, suggest that the actual dose could be significantly reduced from 25 kGy, while maintaining a valid sterility assurance level (SAL) of 10−. The current paper reviews the methods that have been used to develop radiation doses for terminal sterilization of medical products, and the current trend for selection of a specific dose for tissue banks.
Particle production in matrix cosmology

We consider cosmological particle production in 1+1 dimensional string theory. The process is described most efficiently in terms of anomalies, but we also discuss the explicit mode expansions. In matrix cosmology the usual vacuum ambiguity of quantum fields in time-dependent backgrounds is resolved by the underlying matrix model. This leads to a finite energy density for the "in" state which cancels the effect of anomalous particle production.
Adjunctive mild hypothermia therapy to primary percutaneous coronary intervention in patients with ST segment elevation myocardial infarction complicated with cardiogenic shock: A pilot feasibility study.

BACKGROUND
Despite successful primary reperfusion therapy, patients may develop large myocardial infarction related in part to reperfusion injury. Induction of mild therapeutic hypothermia (TH) applied in patients has demonstrated beneficial effect in reducing reperfusion injury. The aim of the study was to evaluate the feasibility and safety of adjunctive mild TH to primary percutaneous coronary intervention (PPCI) in patients with acute ST elevation myocardial infarction (STEMI) complicated with cardiogenic shock (CS).


METHODS
We conducted a prospective single center, open label, historical control study. Patients presenting with STEMI and CS despite maximal support therapy scheduled for PPCI were included. Death was defined as primary endpoint. Secondary outcomes included: TH adverse effect--such as fever, refractory hypotension and arrhythmias, infarct size measured by area under the curve of biomarkers.


RESULTS
Eight consecutive patients were prospectively enrolled (TH group). Thirteen clinically similar patients identified from our database, admitted over 2 years, comprised the historical control group (control group). In the hypothermia group, the mortality was 50% compared with 46% in the control group. There was no difference in the secondary outcomes.


CONCLUSIONS
TH as adjunctive therapy in STEMI patients complicated with CS is feasible and safe. Based on these preliminary observations there appears to be no significant clinical advantage to this form of therapy.
A framework to explore innovation at SAP through bibliometric analysis of patent applications

Easily accessible patent databases and advances in technology have enabled the exploration of organizational innovation through the analysis of patent records. However, the textual content of patents presents obstacles to gleaning useful information. In this study, we develop an expert system framework that utilizes text and data mining procedures for analyzing innovation through textual patent data. Specifically, we use patent titles representing the innovation activity at one company (SAP) and perform a bibliometric analysis using our proposed framework. Enterprise software, of which SAP is a pioneering developer, must serve a wide assortment of functions for companies in many different industries. In addition, SAP’s sole focus is on enterprise software and it is a market leader in the category with substantial patent activity over the last decade. Using our framework to analyze SAP’s patent activity provides a demonstration of how our bibliometric analysis can summarize and identify trends in innovation in a large software company. Our results illustrate that SAP has a breadth of innovative activity spread over the three-tier software engineering architecture and a lack of topical repetition indicative of limited depth. SAP’s innovation is also seen to emphasize data management and quickly integrate emerging technologies. Results of an analysis on any company following our framework could be used for a variety of purposes, including: to examine the scope and scale of innovation of an organization, to examine the influence of technological trends on businesses, or to gain insight into corporate strategy that could be used to aid planning, investment, and purchasing decisions. © 2015 Elsevier Ltd. All rights reserved.
Rapid Eye Movement Sleep Behavior Disorder and Neurodegenerative Disease.

IMPORTANCE
The dream enactment of rapid eye movement sleep behavior disorder (RBD) is often the first indication of an impending α-synuclein disorder, such as Parkinson disease, multiple-system atrophy, or dementia with Lewy bodies.


OBJECTIVE
To provide an overview of RBD from the onset of dream enactment through the emergence of a parkinsonian disorder.


EVIDENCE REVIEW
Peer-reviewed articles, including case reports, case series, retrospective reviews, prospective randomized trials, and basic science investigations, were identified in a PubMed search of articles on RBD from January 1, 1986, through July 31, 2014.


FINDINGS
Under normal conditions, vivid dream mentation combined with skeletal muscle paralysis characterizes rapid eye movement sleep. In RBD, α-synuclein abnormalities in the brainstem disinhibit rapid eye movement sleep motor activity, leading to dream enactment. The behaviors of RBD are often theatrical, with complexity, aggression, and violence; fighting and fleeing actions can be injurious to patients as well as bed partners. Rapid eye movement sleep behavior disorder is distinguished from other parasomnias by clinical features and the demonstration of rapid eye movement sleep without atonia on polysomnography. Consistent with early neurodegeneration, patients with RBD demonstrate subtle motor, cognitive, and autonomic impairments. Approximately 50% of patients with spontaneous RBD will convert to a parkinsonian disorder within a decade. Ultimately, nearly all (81%-90%) patients with RBD develop a neurodegenerative disorder. Among patients with Parkinson disease, RBD predicts a non-tremor-predominant subtype, gait freezing, and an aggressive clinical course. The most commonly cited RBD treatments include low-dose clonazepam or high-dose melatonin taken orally at bedtime.


CONCLUSIONS AND RELEVANCE
Treatment of RBD can prevent injury to patients and bed partners. Because RBD is a prodromal syndrome of Parkinson disease (or related disorder), it represents a unique opportunity for developing and testing disease-modifying therapies.
The effect of fertilizer additions on the solubility and plant-availability of Cd, Ni and Zn in soil

We conducted a pot experiment to investigate the effect of fertilizer additions on the solubility of Cd, Ni and Zn in soil solution and their uptake by plants. Radish (Raphanus sativus cv. Crystal Ball), oat (Avena sativa cv. Thule) and water spinach (Ipomoea aquatica cv. Kangkon) were grown in a naturally metal-rich soil. From day 7 after planting, fertilizers were added daily to each pot. Additions of fertilizer nutrients affected the pH of soil and soil solution, soluble and tissue concentrations of Ca, Mg, K, Cd, Ni and Zn differently in three plant species. The trend of soil and solution pH was in the order: water spinach < radish < oats, that resulted highest soluble and plant tissue concentrations of Cd and Zn in the water spinach followed by radish and then oats. However, Ni concentration in the soil solution increased in all pots and was not affected by pH changes. Soil solution pH increased by more than 1unit in the pots with radish and oats, indicating that mechanisms other than acidification, such as ion exchange and root exudation, may be responsible for the increased heavy metal uptake in these two plant species. Paired t-test showed significantly higher uptake of Cd and Zn in the radish plants resulting in lower concentrations of these elements in the solution. The contribution of mass flow to the supply of major cations and heavy metals varied among elements and plant species. Cadmium, Zn and K were taken up rapidly by all plant species in response to the amount supplied by mass flow. In contrast, the supply of Ni was in excess of its uptake by radish and water spinach. The uptake of all elements was positively correlated (p<0.0001) with mass flow and the transpiration rate in individual plant species. The study suggests that fertilizer cations increased the uptake of metals by improving growth conditions, but the magnitude of increase depended on plant species.
Politics of Place in the Poetry of T. S. Eliot, William Carlos Williams and Marianne Moore

This Ph. D thesis investigates the politics of place in three modernist poets—T. S. Eliot, William Carlos Williams and Marianne Moore. Through the critical lens of both human geography and social construction theories of place, this project aims to uncover the underlying political connotations of the representations of place in their poetry.
The Neuroprotective Peptide Poly-Arginine-12 (R12) Reduces Cell Surface Levels of NMDA NR2B Receptor Subunit in Cortical Neurons; Investigation into the Involvement of Endocytic Mechanisms

We have previously reported that cationic poly-arginine and arginine-rich cell-penetrating peptides display high-level neuroprotection and reduce calcium influx following in vitro excitotoxicity, as well as reduce brain injury in animal stroke models. Using the neuroprotective peptides poly-arginine R12 (R12) and the NR2B9c peptide fused to the arginine-rich carrier peptide TAT (TAT-NR2B9c; also known as NA-1), we investigated the mechanisms whereby poly-arginine and arginine-rich peptides reduce glutamate-induced excitotoxic calcium influx. Using cell surface biotin protein labeling and western blot analysis, we demonstrated that R12 and TAT-NR2B9c significantly reduced cortical neuronal cell surface expression of the NMDA receptor subunit NR2B. Chemical endocytic inhibitors used individually or in combination prior to glutamate excitotoxicity did not significantly affect R12 peptide neuroprotective efficacy. Similarly, pretreatment of neurons with enzymes to degrade anionic cell surface proteoglycans, heparan sulfate proteoglycan (HSPG), and chondroitin sulfate proteoglycan (CSPG), as well as sialic acid residues, did not significantly affect peptide neuroprotective efficacy. While the exact mechanisms responsible for R12 peptide-mediated NMDA receptor NR2B subunit cell surface downregulation were not identified, an endocytic process could not be ruled out. The study supports our hypothesis that arginine-rich peptides reduce excitotoxic calcium influx by reducing the levels of cell surface ion channels.
E-Health Interventions for Suicide Prevention

Many people at risk of suicide do not seek help before an attempt, and do not remain connected to health services following an attempt. E-health interventions are now being considered as a means to identify at-risk individuals, offer self-help through web interventions or to deliver proactive interventions in response to individuals' posts on social media. In this article, we examine research studies which focus on these three aspects of suicide and the internet: the use of online screening for suicide, the effectiveness of e-health interventions aimed to manage suicidal thoughts, and newer studies which aim to proactively intervene when individuals at risk of suicide are identified by their social media postings. We conclude that online screening may have a role, although there is a need for additional robust controlled research to establish whether suicide screening can effectively reduce suicide-related outcomes, and in what settings online screening might be most effective. The effectiveness of Internet interventions may be increased if these interventions are designed to specifically target suicidal thoughts, rather than associated conditions such as depression. The evidence for the use of intervention practices using social media is possible, although validity, feasibility and implementation remains highly uncertain.
Atheroma progression in chronic kidney disease.

BACKGROUND AND OBJECTIVES
Cardiovascular events are 10 to 100 times more frequent in chronic kidney disease (CKD). We tested the hypothesis that the rate of atherosclerotic plaque growth is faster in severe versus moderate CKD.


DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS
We performed a prospective cohort study in 318 prevalent CKD patients with initial creatinine clearance (CCr) between 20 and 50 ml/min/1.73 m(2). Baseline clinical and laboratory data were obtained on all patients. Plaque area was determined every 6 mo using bilateral carotid ultrasonography. Plaque area distribution was normalized using a cube root transformation. Unadjusted and adjusted associations between CCr quintiles and rate of change in the transformed plaque area were assessed using multiple linear regression.


RESULTS
The rate of plaque progression appeared lower in patients with the lowest CCr. Median rate of plaque growth was 0.4 mm(2)/yr in the lowest quintile of CCr (< 23 ml/min/1.73 m(2)) versus 5.0 mm(2)/yr in the highest quintile (> 43 ml/min/1.73 m(2)). This association remained significant after adjustment for potential confounders. A secondary analysis using quintiles of Modification of Diet in Renal Disease (MDRD) GFR confirmed the absence of increased plaque growth at low GFR, although a reduced rate of growth in the lowest quintile of MDRD GFR was not observed.


CONCLUSION
We did not observe accelerated plaque growth at low levels of renal function. We suggest that mechanisms other than plaque growth are responsible for the observed excess of cardiovascular disease in CKD patients.
SENSe: Study of the Effectiveness of Neurorehabilitation on Sensation: a randomized controlled trial.

BACKGROUND
Sensory loss is common after stroke, with negative impact on exploration of the immediate environment, hand function, and return to daily activities.


OBJECTIVE
To compare the effectiveness of a perceptual-learning based sensory discrimination program versus non-specific exposure to sensory stimuli via passive movements and grasping of common objects.


METHODS
The authors conducted a randomized parallel-group controlled trial, with blinding of subjects, clinical assessors, and data analysts. Fifty subjects with impaired texture discrimination, limb position sense, and/or tactile object recognition (>6 weeks, median 48 weeks poststroke) were randomized to receive somatosensory discrimination training (n = 25) or repeated exposure to sensory stimuli (n = 25) in 60-minute sessions for a total of 10 hours. The primary outcome was change in a composite standardized somatosensory deficit (SSD) index following intervention. Follow-up was at 6 weeks and 6 months posttraining.


RESULTS
Between-group comparisons revealed a significantly greater improvement in sensory capacity following sensory discrimination training, t(47) = 2.75, P = .004, 1-tailed; mean between-group change = 11.1 SSD; confidence interval 3.0 to 19.2. Improvements were maintained at 6 weeks and 6 months.


CONCLUSION
Sensory discrimination training can achieve significant improvements in functional sensory discrimination capacity after stroke. The clinically oriented training achieved transfer of training effects to novel stimuli. Our findings provide support for introducing SENSe discrimination training in rehabilitation of sensory deficits after stroke.