LLukas22/scidocs huggingface dataset:
Comparative evaluation of unfixed and fixed human neutrophils for determination of antineutrophil cytoplasmic antibodies by indirect immunofluorescence.

BACKGROUND
Antineutrophil cytoplasmic antibodies (ANCAs) are found in the sera of patients with vasculitides and ulcerative colitis. Using indirect immunofluorescence on ethanol fixed neutrophils, ANCAs can be divided into two types: those that give a cytoplasmic staining pattern (C-ANCA) and those that give a perinuclear staining pattern (P-ANCA). Some studies have indicated that the perinuclear staining pattern might be an artefact of alcohol fixation.


AIMS
To observe any changes seen in the ANCA staining pattern using indirect immunofluorescence on unfixed neutrophils or neutrophils that had been fixed by ethanol, acetone, or paraformaldehyde. In addition, the effects of the different fixation methods on the sensitivity of the indirect immunofluorescence test were evaluated.


METHODS
Twenty one sera from patients with ulcerative colitis and 19 from healthy controls were studied. In addition, 17 sera from patients with vasculitides, including eight with proteinase 3 (PR 3) positive C-ANCA and nine with myeloperoxidase (MPO) positive P-ANCA were included in the study. Antineutrophil cytoplasmic antibodies were analysed by indirect immunofluorescence on unfixed neutrophils or cells fixed by ethanol, acetone, or paraformaldehyde.


RESULTS
All the ulcerative colitis associated ANCA positive sera presented a peri-nuclear staining pattern on both unfixed and fixed cells. The acetone and paraformaldehyde fixations decreased the ulcerative colitis P-ANCA titres. Paraformaldehyde fixation also decreased the MPO positive P-ANCA titres. In indirect immunofluorescence, the staining patterns of all the eight PR 3 positive C-ANCA sera and eight of the nine MPO positive P-ANCA sera did not change, even if unfixed or fixed cells were used.


CONCLUSIONS
The ANCA staining patterns are not affected by the fixation method used, and are the same as when unfixed neutrophils are used; this suggests that the P-ANCA pattern is not an artefact of alcohol fixation. Furthermore, this study confirms that on ethanol fixed neutrophils, the antigen of ulcerative colitis associated P-ANCA is better exposed than on acetone or paraformaldehyde fixed cells.
Kalman Filter Based Adaptive Reduction of Motion Artifact from Photoplethysmographic Signal

Artifact free photoplethysmographic (PPG) signals are necessary for non-invasive estimation of oxygen saturation (SpO2) in arterial blood. Movement of a patient corrupts the PPGs with motion artifacts, resulting in large errors in the computation of Sp02. This paper presents a study on using Kalman Filter in an innovative way by modeling both the Artillery Blood Pressure (ABP) and the unwanted signal, additive motion artifact, to reduce motion artifacts from corrupted PPG signals. Simulation results show acceptable performance regarding LMS and variable step LMS, thus establishing the efficacy of the proposed method. Keywords—Kalman filter, Motion artifact, PPG, Photoplethysmography.
Networks for Code Generation and Semantic Parsing

Syntax Networks for Code Generation and Semantic Parsing Maxim Rabinovich∗ Mitchell Stern∗ Dan Klein Computer Science Division University of California, Berkeley {rabinovich,mitchell,klein}@cs.berkeley.edu
SIMPLE AND SENSITIVE UV SPECTROPHOTOMETRIC METHODS FOR DETERMINATION OF FAMOTIDINE IN TABLET FORMULATIONS

Three new, simple, cost effective, sensitive and accurate UV spectrophotometric methods are described for the determination of famotidine (FMT) in bulk drug and in tablets. The methods are based on measurement of absorbance of FMT in 0.1 M NaOH solution at 286 nm (method A), 0.1 M HCl solution at 265 nm (method B) and in 0.1 M H2SO4 solution at 265 nm (method C). Beer’s law is obeyed over the concentration ranges 0.63 15.0 μg/mL for method A and 1.25 30.0 μg/mL for methods B and C, respectively. The molar absorptivity values are calculated to be 2.14 × 10 L/mol/cm (method A), 1.18 ×10 L/mol/cm (method B) and 1.22 × 10 L/mol/cm (method C) and the corresponding Sandell sensitivity values are 0.016, 0.029 and 0.028 μg/cm. The limits of detection (LOD) and quantification (LOQ) are also reported. Intra-day and inter-day precision, and accuracy of the method were established according to ICH guidelines. The methods were successfully applied to the determination of FMT in tablets and the results were statistically compared with those of the reference method by applying the Student’s t-test and F-test. No interference was observed from the common excipients added to tablets. The accuracy and validity of the method was further ascertained by performing recovery experiments via standard-addition procedure.
Individual and familial factors associated with teenage pregnancy: an interview study.

BACKGROUND
The determinants of teenage sexual health, including pregnancies, can be addressed from social, familial and individual level perspectives. The main objective of this study was to examine whether pregnancy among 18 years old and younger girls were associated with selected individual (age at coitarche, score of sexual health knowledge, dislike of school) and family (mother's education) and family functioning (alcohol abuse in the family, parents' acceptance of sexual relationship) characteristics.


METHODS
An interview survey in two medical institutions in Estonia among 279 18 year old and younger girls, who: (i) used contraception, had been sexually active for at least 6 months and had not pregnancies--(148 girls); (ii) came for termination of pregnancy--abortion group; (iii) planned to deliver and came for prenatal care--delivery group. The last two groups were analysed together as the 'pregnancy group'--131 girls. Multivariate analysis, by means of logistic regression models, was used to explore whether the associations were sustained after adjusting for other variables. Crude odds ratios (ORs), adjusted ORs and their 95% confidence intervals (CIs) were estimated, with girls having no pregnancies as the reference group.


RESULTS
Risk factors associated with teenage pregnancy were low score of sexual health knowledge (adjusted ORs 3.07; 95% CIs 1.73-5.46), dislike of school (adjusted ORs 1.96; 95% CIs 1.08-3.54), alcohol abuse by family members (adjusted ORs 2.03; 95% CIs 1.16-3.54).


CONCLUSION
Sexual knowledge of teenagers, their attitude towards school, alcohol abuse in the family are factors associated with teenage pregnancies.
MaltParser: A Language-Independent System for Data-Driven Dependency Parsing

One of the potential advantages of data-driven approaches to natural language processing is that they can be ported to new languages, provided that the necessary linguistic data resources are available. In practice, this advantage can be hard to realize if models are overfitted to a particular language or linguistic annotation scheme. Thus, using two state-of-the-art statistical parsers developed for English to parse Italian, Corazza et al. [6] report an increase in error rate of 15–18%, and similar results have been reported for other languages [5, 1, 9, 14]. To overcome this kind of problem, systems for data-driven processing need to be designed for flexible reconfiguration, not only with respect to the selection of linguistic features but also with respect to algorithms and learning methods. In this paper, we present a data-driven approach to dependency parsing that has been applied to several languages, consistently giving a dependency accuracy of 80–90% without any language-specific enhancements and with fairly modest data resources. The methodology is based on three essential components:
Brief announcement: deadline-aware scheduling of big-data processing jobs

This paper presents a novel algorithm for scheduling big data jobs on large compute clusters. In our model, each job is represented by a DAG consisting of several stages linked by precedence constraints. The resource allocation per stage is malleable, in the sense that the processing time of a stage depends on the resources allocated to it (the dependency can be arbitrary in general).The goal of the scheduler is to maximize the total value of completed jobs, where the value for each job depends on its completion time. We design an algorithm for the problem which guarantees an expected constant approximation factor when the cluster capacity is sufficiently high. To the best of our knowledge, this is the first constant-factor approximation algorithm for the problem. The algorithm is based on formulating the problem as a linear program and then rounding an optimal (fractional) solution into a feasible (integral) schedule using randomized rounding.
Superfluousness of motor innervation for the formation of muscle spindles in neonatal rats

Muscle spindles form de novo in reinnervated muscles of neonatal rats treated with nerve growth factor. Whether the spindles can also form in muscle reinnervated only by afferents was investigated by removing the lumbosacral segment of the spinal cord immediately after crushing the nerve to the medial gastrocnemius muscle at birth, and administering nerve growth factor for 10 days afterwards. As predicted, the medial gastrocnemius muscles were reinnervated by afferents, but not efferents. No motor endplates were visible on any muscle fibers, and extrafusal fibers were atrophied. The reinnervated muscles contained spindle-like encapsulations of one to four fibers at 5, 7, 9 and 30 days after the nerve crush. The number of spindles as well as encapsulated fibers exceeded that of normal medial gastrocnemius muscles. The encapsulated fibers resembled typical intrafusal fibers. They had normal sensory-muscle contacts, but no motor endings. The fibers displayed equatorial clusters of myonuclei and expressed the spindle-specific slow-tonic myosin heavy chain isoform at postnatal day 30. Thus, efferents are not essential for the formation and differentiation of muscle spindles in reinnervated muscles of neonatal rats.
Global and regional burden of disease and risk factors, 2001: systematic analysis of population health data

BACKGROUND
Our aim was to calculate the global burden of disease and risk factors for 2001, to examine regional trends from 1990 to 2001, and to provide a starting point for the analysis of the Disease Control Priorities Project (DCPP).


METHODS
We calculated mortality, incidence, prevalence, and disability adjusted life years (DALYs) for 136 diseases and injuries, for seven income/geographic country groups. To assess trends, we re-estimated all-cause mortality for 1990 with the same methods as for 2001. We estimated mortality and disease burden attributable to 19 risk factors.


FINDINGS
About 56 million people died in 2001. Of these, 10.6 million were children, 99% of whom lived in low-and-middle-income countries. More than half of child deaths in 2001 were attributable to acute respiratory infections, measles, diarrhoea, malaria, and HIV/AIDS. The ten leading diseases for global disease burden were perinatal conditions, lower respiratory infections, ischaemic heart disease, cerebrovascular disease, HIV/AIDS, diarrhoeal diseases, unipolar major depression, malaria, chronic obstructive pulmonary disease, and tuberculosis. There was a 20% reduction in global disease burden per head due to communicable, maternal, perinatal, and nutritional conditions between 1990 and 2001. Almost half the disease burden in low-and-middle-income countries is now from non-communicable diseases (disease burden per head in Sub-Saharan Africa and the low-and-middle-income countries of Europe and Central Asia increased between 1990 and 2001). Undernutrition remains the leading risk factor for health loss. An estimated 45% of global mortality and 36% of global disease burden are attributable to the joint hazardous effects of the 19 risk factors studied. Uncertainty in all-cause mortality estimates ranged from around 1% in high-income countries to 15-20% in Sub-Saharan Africa. Uncertainty was larger for mortality from specific diseases, and for incidence and prevalence of non-fatal outcomes.


INTERPRETATION
Despite uncertainties about mortality and burden of disease estimates, our findings suggest that substantial gains in health have been achieved in most populations, countered by the HIV/AIDS epidemic in Sub-Saharan Africa and setbacks in adult mortality in countries of the former Soviet Union. Our results on major disease, injury, and risk factor causes of loss of health, together with information on the cost-effectiveness of interventions, can assist in accelerating progress towards better health and reducing the persistent differentials in health between poor and rich countries.
Biophysical processes supporting the diversity of microbial life in soil

Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
Neuroanatomical abnormalities that predate the onset of psychosis: a multicenter study.

CONTEXT
People experiencing possible prodromal symptoms of psychosis have a very high risk of developing the disorder, but it is not possible to predict, on the basis of their presenting clinical features, which individuals will subsequently become psychotic. Recent neuroimaging studies suggest that there are volumetric differences between individuals at ultra-high risk (UHR) for psychosis who later develop psychotic disorder and those who do not. However, the samples examined to date have been small, and the findings have been inconsistent.


OBJECTIVE
To assess brain structure in individuals at UHR for psychosis in a larger and more representative sample than in previous studies by combining magnetic resonance imaging data from 5 different scanning sites.


DESIGN
Case-control study.


SETTING
Multisite.


PARTICIPANTS
A total of 182 individuals at UHR and 167 healthy controls. Participants were observed clinically for a mean of 2 years. Forty-eight individuals (26.4%) in the UHR group developed psychosis and 134 did not.


MAIN OUTCOME MEASURES
Magnetic resonance images were acquired from each participant. Group differences in gray matter volume were examined using optimized voxel-based morphometry.


RESULTS
The UHR group as a whole had less gray matter volume than did controls in the frontal regions bilaterally. The UHR subgroup who later developed psychosis had less gray matter volume in the left parahippocampal cortex than did the UHR subgroup who did not.


CONCLUSIONS
Individuals at high risk for psychosis show alterations in regional gray matter volume regardless of whether they subsequently develop the disorder. In the UHR population, reduced left parahippocampal volume was specifically associated with the later onset of psychosis. Alterations in this region may, thus, be crucial to the expression of illness. Identifying abnormalities that specifically predate the onset of psychosis informs the development of clinical investigations designed to predict which individuals at high risk will subsequently develop the disorder.
A cloud approach to unified lifecycle data management in architecture, engineering, construction and facilities management: Integrating BIMs and SNS

The problem of data integration throughout the lifecycle of a construction project among multiple collaborative enterprises remains unsolved due to the dynamics and fragmented nature of the construction industry. This study presents a novel cloud approach that, focusing on China’s special construction requirements, proposes a series of as-built BIM (building information modeling) tools and a self-organised application model that correlates project engineering data and project management data through a seamless BIM and BSNS (business social netwo rking services) federation. To achieve a logically centralised single-source data structure, a unified data model is constructed that integrates two categories of heterogeneous databas es through the adoption of handlers. Based on these models, key technical mechanisms that are critical to the successful management of large amounts of data are proposed and implemented, including permission, data manipulation and file version control. Specifically, a dynamic Generalised List series is proposed to address the sophisticated construction file versioning issue. The proposed cloud has been successfully used in real applications in China. This research work can enable data sharing not only by individuals and project teams but also by enterprises in a consistent and sustainable way throughout the life of a construction project. This system will reduce costs for construction firms by providing effective and efficient means and guides to comp lex project management, and by facilitating the conversion of project data into enterprise-owned properties. 2012 Elsevier Ltd. All rights reserved.
Internal crowdsourcing: conceptual framework, structured review, and research agenda

The use of IT-enabled crowdsourcing with employees in enterprises has increased substantially in recent years. This phenomenon, which we refer to as ‘internal crowdsourcing’, is distinct both from external crowdsourcing with end users and from hierarchy-based work with employees. A literature stream has emerged that corresponds with the increased relevance of internal crowdsourcing in practice. The purpose of this review paper of internal crowdsourcing is to provide conceptual development, synthesise the literature, and provide a research agenda. In the review reported in this paper, we systematically analysed and critically reviewed the literature in this domain published thus far (74 papers). We found useful findings and insights into a new and relevant IT-enabled phenomenon. At the same time, we also found conflicting definitions and conceptualisation, as well as research efforts that are not well integrated. The paper supports future research on internal crowdsourcing by providing improved conceptualisation, consolidating insights, and identifying important areas for future research. Journal of Information Technology (2016) 31, 166–184. doi:10.1057/jit.2016.14
Stock market prediction using Hidden Markov Models

Stock market prediction is a classic problem which has been analyzed extensively using tools and techniques of Machine Learning. Interesting properties which make this modeling non-trivial is the time dependence, volatility and other similar complex dependencies of this problem. To incorporate these, Hidden Markov Models (HMM's) have recently been applied to forecast and predict the stock market. We present the Maximum a Posteriori HMM approach for forecasting stock values for the next day given historical data. In our approach, we consider the fractional change in Stock value and the intra-day high and low values of the stock to train the continuous HMM. This HMM is then used to make a Maximum a Posteriori decision over all the possible stock values for the next day. We test our approach on several stocks, and compare the performance to some of the existing methods using HMMs and Artificial Neural Networks using Mean Absolute Percentage Error (MAPE).
A phase II trial of S-1 and cisplatin in patients with metastatic or relapsed biliary tract cancer.

BACKGROUND
Optimal chemotherapy for advanced biliary tract cancer (BTC) is yet to be defined. We carried out this study to evaluate the efficacy and toxicity of combination chemotherapy with S-1 and cisplatin in metastatic or relapsed BTC.


PATIENTS AND METHODS
Patients with pathologically proven BTC were eligible. The chemotherapy regimen consisted of S-1 (40 mg/m(2) p.o. b.i.d. from D1-14) and cisplatin (60 mg/m(2) on D1), repeated every 3 weeks.


RESULTS
Fifty-one BTC patients (metastatic:relapsed = 37:14, Gall-bladder:intrahepatic bile ducts:extrahepatic bile ducts = 16:25:10) were enrolled from January 2005 to December 2006. Median age was 57 years (range, 31-71) and most patients had a good performance status. The overall response rate was 30% [95% confidence interval (CI), 17.3-42.7] and complete response was observed in two patients (4%), partial response in 13 (26%), stable disease in 21 (42%), and progressive disease in 9 (18%). With a median follow-up of 12.4 months, the median time to progression was 4.8 months (95% CI, 3.3-6.3) and median overall survival was 8.7 months (95% CI, 6.0-11.4). Major toxic effects were grade 3/4 neutropenia (8.9% of all cycles) and febrile neutropenia was observed in six cycles (2.7% of all cycles).


CONCLUSION
Combination chemotherapy with S-1 and cisplatin was a moderately effective outpatient-based regimen in BTC patients. Toxic effects were moderate but manageable.
Event Processing in Sensor Streams

Sensors including RFID tags have been widely deployed for measuring environmental parameters such as temperature, humidity, oxygen concentration, monitoring the location and velocity of moving objects, tracking tagged objects, and many others. To support effective, efficient, and near real-time phenomena probing and objects monitoring, streaming sensor data have to be gracefully managed in an event processing manner. Different from the traditional events, sensor events come with temporal or spatio-temporal constraints and can be non-spontaneous. Meanwhile, like general event streams, sensor event streams can be generated with very high volumes and rates. Primitive sensor events need to be filtered, aggregated and correlated to generate more semantically rich complex events to facilitate the requirements of up-streaming applications. Motivated by such challenges, many new methods have been proposed in the past to support event processing in sensor event streams. In this chapter, we survey state-of-the-art research on event processing in sensor networks, and provide a broad overview of major topics in Springer Science+Business Media New York 2013 © Managing and Mining Sensor Data, DOI 10.1007/978-1-4614-6309-2_4, C.C. Aggarwal (ed.), 77 78 MANAGING AND MINING SENSOR DATA complex RFID event processing, including event specification languages, event detection models, event processing methods and their optimizations. Additionally, we have presented an open discussion on advanced issues such as processing uncertain and out-of-order sensor events.