LLukas22/scidocs huggingface dataset:
PCA for large data sets with parallel data summarization

Parallel processing is essential for large-scale analytics. Principal Component Analysis (PCA) is a well known model for dimensionality reduction in statistical analysis, which requires a demanding number of I/O and CPU operations. In this paper, we study how to compute PCA in parallel. We extend a previous sequential method to a highly parallel algorithm that can compute PCA in one pass on a large data set based on summarization matrices. We also study how to integrate our algorithm with a DBMS; our solution is based on a combination of parallel data set summarization via user-defined aggregations and calling the MKL parallel variant of the LAPACK library to solve Singular Value Decomposition (SVD) in RAM. Our algorithm is theoretically shown to achieve linear speedup, linear scalability on data size, quadratic time on dimensionality (but in RAM), spending most of the time on data set summarization, despite the fact that SVD has cubic time complexity on dimensionality. Experiments with large data sets on multicore CPUs show that our solution is much faster than the R statistical package as well as solving PCA with SQL queries. Benchmarking on multicore CPUs and a parallel DBMS running on multiple nodes confirms linear speedup and linear scalability.
Facial expression recognition based on Local Binary Patterns: A comprehensive study

Automatic facial expression analysis is an interesting and challenging problem, and impacts important applications in many areas such as human–computer interaction and data-driven animation. Deriving an effective facial representation from original face images is a vital step for successful facial expression recognition. In this paper, we empirically evaluate facial representation based on statistical local features, Local Binary Patterns, for person-independent facial expression recognition. Different machine learning methods are systematically examined on several databases. Extensive experiments illustrate that LBP features are effective and efficient for facial expression recognition. We further formulate Boosted-LBP to extract the most discriminant LBP features, and the best recognition performance is obtained by using Support Vector Machine classifiers with Boosted-LBP features. Moreover, we investigate LBP features for low-resolution facial expression recognition, which is a critical problem but seldom addressed in the existing work. We observe in our experiments that LBP features perform stably and robustly over a useful range of low resolutions of face images, and yield promising performance in compressed low-resolution video sequences captured in real-world environments. 2008 Elsevier B.V. All rights reserved.
Hemorrhagic complications in a phase II study of sunitinib in patients of nasopharyngeal carcinoma who has previously received high-dose radiation.

BACKGROUND
We aimed to evaluate the safety and efficacy of single-agent sunitinib in nasopharyngeal carcinoma (NPC).


METHODS
Eligible patients had progressive disease after prior platinum-based chemotherapy. Sunitinib was given as continuous once-daily dosing of 37.5 mg in 4-week cycles until progression.


RESULTS
Thirteen patients were enrolled. Recruitment was stopped after two patients died of hemorrhagic events. All patients had previously received curative radiotherapy (RT) to nasopharynx/neck (including nine patients who had chemoradiotherapy). Patients received a median of three cycles of sunitinib. One patient was still on sunitinib with stable disease after 24 cycles. Hemorrhagic events occurred in nine patients (64%), including epistaxis in six, hemoptyses in three and hematemesis in two patients. Prior RT to thorax was significantly associated with hemoptyses (P = 0.03). Two patients with local tumor invasion into the carotid sheath developed fatal epistaxis/hematemesis within the first cycle of sunitinib, likely due to internal carotid blowout after tumor shrinkage.


CONCLUSIONS
Sunitinib demonstrated modest clinical activity in heavily pretreated NPC patients. However, the high incidence of hemorrhage from the upper aerodigestive tract in NPC patients who received prior high-dose RT to the region is of concern. Direct vascular invasion by tumors appeared to increase the risk of serious bleeding.
Tramadol/paracetamol combination tablet for postoperative pain following ambulatory hand surgery: a double-blind, double-dummy, randomized, parallel-group trial

This randomized, double-blind, double-dummy, multicenter trial compared efficacy and safety of tramadol HCL 37.5 mg/paracetamol 325 mg combination tablet with tramadol HCL 50 mg capsule in the treatment of postoperative pain following ambulatory hand surgery with iv regional anesthesia. Patients received trial medication at admission, immediately after surgery, and every 6 hours after discharge until midnight of the first postoperative day. Analgesic efficacy was assessed by patients (n = 128 in each group, full analysis set) and recorded in a diary on the evening of surgery day and of the first postoperative day. They also documented the occurrence of adverse events. By the end of the first postoperative day, the proportion of treatment responders based on treatment satisfaction (primary efficacy variable) was comparable between the groups (78.1% combination, 71.9% tramadol; P = 0.24) and mean pain intensity (rated on a numerical scale from 0 = no pain to 10 = worst imaginable pain) had been reduced to 1.7 ± 2.0 for both groups. Under both treatments, twice as many patients experienced no pain (score = 0) on the first postoperative day compared to the day of surgery (35.9% vs 16.4% for tramadol/paracetamol and 36.7% vs 18% for tramadol treatment). Rescue medication leading to withdrawal (diclofenac 50 mg) was required by 17.2% patients with tramadol/paracetamol and 13.3% with tramadol. Adverse events (mainly nausea, dizziness, somnolence, vomiting, and increased sweating) occurred less frequently in patients under combination treatment (P = 0.004). Tramadol/paracetamol combination tablets provided comparable analgesic efficacy with a better safety profile to tramadol capsules in patients experiencing postoperative pain following ambulatory hand surgery.
High Sensitivity MEMS Strain Sensor: Design and Simulation

In this article, we report on the new design of a miniaturized strain microsensor. The proposed sensor utilizes the piezoresistive properties of doped single crystal silicon. Employing the Micro Electro Mechanical Systems (MEMS) technology, high sensor sensitivities and resolutions have been achieved. The current sensor design employs different levels of signal amplifications. These amplifications include geometric, material and electronic levels. The sensor and the electronic circuits can be integrated on a single chip, and packaged as a small functional unit. The sensor converts input strain to resistance change, which can be transformed to bridge imbalance voltage. An analog output that demonstrates high sensitivity (0.03mV/me), high absolute resolution (1μe) and low power consumption (100μA) with a maximum range of ±4000μe has been reported. These performance characteristics have been achieved with high signal stability over a wide temperature range (±50oC), which introduces the proposed MEMS strain sensor as a strong candidate for wireless strain sensing applications under harsh environmental conditions. Moreover, this sensor has been designed, verified and can be easily modified to measure other values such as force, torque…etc. In this work, the sensor design is achieved using Finite Element Method (FEM) with the application of the piezoresistivity theory. This design process and the microfabrication process flow to prototype the design have been presented.
Experimental Demonstration of Vertical ${\rm Cu}\hbox{-}{\rm SiO}_{2}\hbox{-}{\rm Si}$ Hybrid Plasmonic Waveguide Components on an SOI Platform

Vertical Cu-SiO2-Si hybrid plasmonic waveguides (HPWs) along with various passive components are fabricated on a silicon-on-insulator platform using standard complementary metal-oxide-semiconductor (CMOS) technology and characterized at 1550-nm telecommunication wavelengths. The HPW exhibits relatively low propagation loss of ~0.12 dB/μm and high coupling efficiency of ~86% with the conventional Si strip waveguide. A plasmonic waveguide-ring resonator with 1.09-μm radius exhibits extinction ratio of ~13.7 dB, free spectral range of ~106 nm, and Q-factor of ~63. These superior performances together with the CMOS compatibility make the HPW an attractive candidate for future dense Si nanophotonic integrated circuits.
The frequent and conserved DR3-B8-A1 extended haplotype confers less diabetes risk than other DR3 haplotypes.

AIM
The goal of this study was to develop and implement methodology that would aid in the analysis of extended high-density single nucleotide polymorphism (SNP) major histocompatibility complex (MHC) haplotypes combined with human leucocyte antigen (HLA) alleles in relation to type 1 diabetes risk.


METHODS
High-density SNP genotype data (2918 SNPs) across the MHC from the Type 1 Diabetes Genetics Consortium (1240 families), in addition to HLA data, were processed into haplotypes using PedCheck and Merlin, and extended DR3 haplotypes were analysed.


RESULTS
With this large dense set of SNPs, the conservation of DR3-B8-A1 (8.1) haplotypes spanned the MHC (>/=99% SNP identity). Forty-seven individuals homozygous for the 8.1 haplotype also shared the same homozygous genotype at four 'sentinel' SNPs (rs2157678 'T', rs3130380 'A', rs3094628 'C' and rs3130352 'T'). Conservation extended from HLA-DQB1 to the telomeric end of the SNP panels (3.4 Mb total). In addition, we found that the 8.1 haplotype is associated with lower risk than other DR3 haplotypes by both haplotypic and genotypic analyses [haplotype: p = 0.009, odds ratio (OR) = 0.65; genotype: p = 6.3 x 10(-5), OR = 0.27]. The 8.1 haplotype (from genotypic analyses) is associated with lower risk than the high-risk DR3-B18-A30 haplotype (p = 0.01, OR = 0.23), but the DR3-B18-A30 haplotype did not differ from other non-8.1 DR3 haplotypes relative to diabetes association.


CONCLUSION
The 8.1 haplotype demonstrates extreme conservation (>3.4 Mb) and is associated with significantly lower risk for type 1 diabetes than other DR3 haplotypes.
Frictions in Shadow Banking: Evidence from the Lending Behavior of Money Market Mutual Funds

We document frictions in money market mutual fund lending that lead to the transmission of distress across borrowers. Using novel security-level holdings data, we show that funds with exposure to Eurozone banks suffered large outflows in mid-2011. These outflows had significant spillovers: non-European issuers relying on such funds raised less short-term debt financing. Issuer characteristics do not explain the results: holding fixed the issuer, funds with higher Eurozone exposure cut lending more. Due to credit market frictions, funds with low Eurozone exposure provided substitute financing only to issuers they had pre-existing relationships with, even though issuers are large, highly-rated firms. JEL G01, G18, G21, G28, G32 ∗This paper was previously circulated under the title “The Quiet Run of 2011: Money Market Mutual Funds and the European Debt Crisis.” We thank Susan Christoffersen (discussant), Isil Erel, Robin Greenwood, Sam Hanson, Victoria Ivashina, Andrew Karolyi (editor), Patrick McCabe, Morgan Ricks, David Scharfstein, Alexander Schulz (discussant), Jeremy Stein, René Stulz, Krista Schwarz (discussant), Mike Weisbach, two anonymous referees, and seminar participants at the Bank of Canada/Bank of Spain workshop on International Financial Markets, 2012 EFA Annual Meetings, the Federal Reserve Board, Harvard Business School, the Ohio State University, and 2013 WFA Annual Meetings for helpful comments, and Pete Crane for discussing the money markets with us.
Long-term prognosis of HIV-infected patients with Kaposi sarcoma treated with pegylated liposomal doxorubicin.

INTRODUCTION
Incidence of Kaposi sarcoma (KS) in human immunodeficiency virus (HIV)-infected persons has dramatically decreased in the highly active antiretroviral therapy era. However, this tumor still represents the most common cancer in this population.


OBJECTIVES
The objectives of this study were to evaluate long-term prognosis of HIV-infected patients with KS who had received pegylated liposomal doxorubicin (PLD) and, more specifically, to assess tumor relapse rate, mortality, and cause of death in these subjects.


DESIGN
This study was a retrospective review of all patients with KS who had received PLD in centers belonging to the Caelyx/KS Spanish Group. Kaplan-Meier analysis and univariate and multivariate Cox-regression analysis were used to assess the rate of and factors associated with relapse and death through January 2006.


RESULTS
A total of 98 patients received PLD from September 1997 through June 2002. Median follow-up after initiation of treatment was 28.7 months (interquartile range, 6.6-73.2 months); during follow-up, 29 patients died (a mortality rate of 14.6% per year). In 9 patients (31%), the cause of death was related to the appearance of other tumors (including 7 lymphomas, 1 gastrointestinal adenocarcinoma, and 1 tongue epidermoid cancer). Death caused by progression of KS occurred in 3 cases. Death risk was inversely related to CD4(+) cell counts at the end of follow-up (hazard ratio for every increase in CD4(+) cell count of 100 cells/microL, 0.7; 95% confidence interval, 0.5-0.9). A relapse study was performed for 61 patients who had complete or partial response to PLD and who attended a control visit after treatment completion. After a median follow-up of 50 months (interquartile range, 17.2-76 months), 8 patients (13%) had experienced relapse; 5 of these patient experienced relapse within the first year after stopping PLD. The only factor that was independently related to risk of relapse was having a CD4(+) cell count >200 cells/microL at baseline (hazard ratio, 6.2; 95% confidence interval, 1.2-30). Lower CD4(+) cell count at the end of follow-up was marginally associated with relapse (hazard ratio for every increase in CD4(+) cell count of 100 cells/microL, 0.7; 95% confidence interval, 0.6-1.01).


CONCLUSIONS
Treatment of KS with PLD in HIV-infected patients is followed by a low relapse rate, with most relapses occurring during the first year after stopping chemotherapy. However, the mortality rate in this population was high, in part because of an unexpectedly high incidence of other tumors, mainly lymphomas.
Motion Planning in Dynamic Environments: Obstacles Moving Along Arbitrary Trajectories

This paper generalizes the concept of velocity obstacles [3] to obstacles moving along arbitrary trajectories. We introduce the non-linear velocity obstacle, which takes into account the shape, velocity and path curvature of the moving obstacle. The non-linear v-obstacle allows selecting a single avoidance maneuver (if one exists) that avoids any number of obstacles moving on any known trajectories. For unknown trajectories, the non-linear v-obstacles can be used to generate local avoidance maneuvers based on the current velocity and path curvature of the moving obstacle. This elevates the planning strategy to a second order method, compared to the first order avoidance using the linear v-obstacle, and zero order avoidance using only position information. Analytic expressions for the non-linear v-obstacle are derived for general trajectories in the plane. The nonlinear v-obstacles are demonstrated in a complex traffic example.
Goal Profiles, Mental Toughness and its Influence on Performance Outcomes among Wushu Athletes.

This study examined the association between goal orientations and mental toughness and its influence on performance outcomes in competition. Wushu athletes (n = 40) competing in Intervarsity championships in Malaysia completed Task and Ego Orientations in Sport Questionnaire (TEOSQ) and Psychological Performance Inventory (PPI). Using cluster analysis techniques including hierarchical methods and the non-hierarchical method (k-means cluster) to examine goal profiles, a three cluster solution emerged viz. cluster 1 - high task and moderate ego (HT/ME), cluster 2 - moderate task and low ego (MT/LE) and, cluster 3 - moderate task and moderate ego (MT/ME). Analysis of the fundamental areas of mental toughness based on goal profiles revealed that athletes in cluster 1 scored significantly higher on negative energy control than athletes in cluster 2. Further, athletes in cluster 1 also scored significantly higher on positive energy control than athletes in cluster 3. Chi-square (χ(2)) test revealed no significant differences among athletes with different goal profiles on performance outcomes in the competition. However, significant differences were observed between athletes (medallist and non medallist) in self- confidence (p = 0.001) and negative energy control (p = 0.042). Medallist's scored significantly higher on self-confidence (mean = 21.82 ± 2.72) and negative energy control (mean = 19.59 ± 2.32) than the non-medallists (self confidence-mean = 18.76 ± 2.49; negative energy control mean = 18.14 ± 1.91). Key pointsMental toughness can be influenced by certain goal profile combination.Athletes with successful outcomes in performance (medallist) displayed greater mental toughness.
The "syncope and dementia" study: a prospective, observational, multicenter study of elderly patients with dementia and episodes of "suspected" transient loss of consciousness.

BACKGROUND AND AIM
Syncope and related falls are one of the main causes and the predominant cause of hospitalization in elderly patients with dementia. However, the diagnostic protocol for syncope is difficult to apply to patients with dementia. Thus, we developed a "simplified" protocol to be used in a prospective, observational, and multicenter study in elderly patients with dementia and transient loss of consciousness suspected for syncope or unexplained falls. Here, we describe the protocol, its feasibility and the characteristics of the patients enrolled in the study.


METHODS
Patients aged ≥65 years with a diagnosis of dementia and one or more episodes of transient loss of consciousness during the previous 3 months, subsequently referred to a Geriatric Department in different regions of Italy, from February 2012 to May 2014, were enrolled. A simplified protocol was applied in all patients. Selected patients underwent a second-level evaluation.


RESULTS
Three hundred and three patients were enrolled; 52.6% presented with episodes suspected to be syncope, 44.5% for unexplained fall and 2.9% both. Vascular dementia had been previously diagnosed in 53.6% of participants, Alzheimer's disease in 23.5% and mixed forms in 12.6%. Patients presented with high comorbidity (CIRS score = 3.6 ± 2), severe functional impairment, (BADL lost = 3 ± 2), and polypharmacy (6 ± 3 drugs).


CONCLUSION
Elderly patients with dementia enrolled for suspected syncope and unexplained falls have high comorbidity and disability. The clinical presentation is often atypical and the presence of unexplained falls is particularly frequent.
Can the Quality of Pearls from the Japanese Pearl Oyster (Pinctada fucata) be Explained by the Gene Expression Patterns of the Major Shell Matrix Proteins in the Pearl Sac?

For pearl culture, the pearl oyster is forced open and a nucleus is implanted into the gonad with a mantle graft. The outer mantle epithelial cells of the implanted mantle graft elongate and surrounding the nucleus a pearl sac is formed. Shell matrix proteins secreted by the pearl sac play an important role in the regulation of pearl formation. Recently, seven shell matrix proteins were identified from the pearl oyster Pinctada fucata. However, there is a paucity of information on the function of these proteins and their gene expression patterns. Our study aims to elucidate the relationship between pearl type, quality, and gene expression patterns of six shell matrix proteins (msi60, n16, nacrein, msi31, prismalin-14, and aspein) in the pearl sac based on real-time PCR analysis. After culturing for about 2 months, the pearl sac tissues were collected from 22 individuals: 12 with high quality (HP), nine with low quality (LP), and one with organic (ORG) pearl formation. The surface of each of the 12 HP pearls was composed only of a nacreous layer; in contrast, that of the nine LP pearls was composed of nacreous and prismatic layers. The six target gene expressions were detected in all individuals. However, delta threshold cycle (ΔC T) for msi31 was significantly higher in the HP than in the LP individuals (Mann–Whitney’s U test, p = 0.02). This means that the relative expression level of msi31, which constitutes the framework of the prismatic layer, was higher in the LP than in the HP individuals.
Why the Diagnosis of Attention Deficit Hyperactivity Disorder Matters

BACKGROUND
Attention Deficit Hyperactivity disorder (ADHD) is one of the most common and challenging childhood neurobehavioral disorders. ADHD is known to negatively impact children, their families, and their community. About one-third to one-half of patients with ADHD will have persistent symptoms into adulthood. The prevalence in the United States is estimated at 5-11%, representing 6.4 million children nationwide. The variability in the prevalence of ADHD worldwide and within the US may be due to the wide range of factors that affect accurate assessment of children and youth. Because of these obstacles to assessment, ADHD is under-diagnosed, misdiagnosed, and undertreated.


OBJECTIVES
We examined factors associated with making and receiving the diagnosis of ADHD. We sought to review the consequences of a lack of diagnosis and treatment for ADHD on children's and adolescent's lives and how their families and the community may be involved in these consequences.


METHODS
We reviewed scientific articles looking for factors that impact the identification and diagnosis of ADHD and articles that demonstrate naturalistic outcomes of diagnosis and treatment. The data bases PubMed and Google scholar were searched from the year 1995 to 2015 using the search terms "ADHD, diagnosis, outcomes." We then reviewed abstracts and reference lists within those articles to rule out or rule in these or other articles.


RESULTS
Multiple factors have significant impact in the identification and diagnosis of ADHD including parents, healthcare providers, teachers, and aspects of the environment. Only a few studies detailed the impact of not diagnosing ADHD, with unclear consequences independent of treatment. A more significant number of studies have examined the impact of untreated ADHD. The experience around receiving a diagnosis described by individuals with ADHD provides some additional insights.


CONCLUSION
ADHD diagnosis is influenced by perceptions of many different members of a child's community. A lack of clear understanding of ADHD and the importance of its diagnosis and treatment still exists among many members of the community including parents, teachers, and healthcare providers. More basic and clinical research will improve methods of diagnosis and information dissemination. Even before further advancements in science, strong partnerships between clinicians and patients with ADHD may be the best way to reduce the negative impacts of this disorder.