LLukas22/scidocs huggingface dataset:
Long read alignment based on maximal exact match seeds

MOTIVATION
The explosive growth of next-generation sequencing datasets poses a challenge to the mapping of reads to reference genomes in terms of alignment quality and execution speed. With the continuing progress of high-throughput sequencing technologies, read length is constantly increasing and many existing aligners are becoming inefficient as generated reads grow larger.


RESULTS
We present CUSHAW2, a parallelized, accurate, and memory-efficient long read aligner. Our aligner is based on the seed-and-extend approach and uses maximal exact matches as seeds to find gapped alignments. We have evaluated and compared CUSHAW2 to the three other long read aligners BWA-SW, Bowtie2 and GASSST, by aligning simulated and real datasets to the human genome. The performance evaluation shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads.


AVAILABILITY
CUSHAW2, written in C++, and all simulated datasets are available at http://cushaw2.sourceforge.net


CONTACT
liuy@uni-mainz.de; bertil.schmidt@uni-mainz.de


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Initial lymphocyte count and low BMI may affect fingolimod-induced lymphopenia.

OBJECTIVE
To assess whether pretreatment-lymphocyte counts, treatment before fingolimod, age, sex, or body mass index (BMI) affects the risk of fingolimod-induced lymphopenia in patients with relapsing-remitting multiple sclerosis (RRMS).


METHODS
Data were obtained from a German multicenter, single-arm, open-label study of patients with RRMS treated with fingolimod, and findings were validated in an independent Swedish national pharmacovigilance study.


RESULTS
Four hundred eighteen patients with RRMS from Germany and 438 patients from Sweden were included. A nadir ≤0.2 × 10(9) lymphocytes/L was reached in 15% (95% confidence interval [CI] 12%-17%) of all 856 patients. Patients with lower starting lymphocyte counts (below 1.6 × 10(9)/L) and patients with BMI lower than 18.5 kg/m(2) (women only) were at higher risk of developing lymphopenia with values ≤0.2 × 10(9)/L in the combined analysis, increasing the risk in these subgroups to 26% (95% CI 20%-31%) or 46% (95% CI 23%-71%), respectively. In the German cohort, infection rates were similar in patients who developed severe lymphopenia and those who did not.


CONCLUSIONS
Our findings suggest that patients with low baseline lymphocyte counts and underweight women in which fingolimod treatment will be initiated should possibly be monitored more closely.
Coordinated reset neuromodulation for Parkinson's disease: Proof-of-concept study

BACKGROUND
The discovery of abnormal synchronization of neuronal activity in the basal ganglia in Parkinson's disease (PD) has prompted the development of novel neuromodulation paradigms. Coordinated reset neuromodulation intends to specifically counteract excessive synchronization and to induce cumulative unlearning of pathological synaptic connectivity and neuronal synchrony.


METHODS
In this prospective case series, six PD patients were evaluated before and after coordinated reset neuromodulation according to a standardized protocol that included both electrophysiological recordings and clinical assessments.


RESULTS
Coordinated reset neuromodulation of the subthalamic nucleus (STN) applied to six PD patients in an externalized setting during three stimulation days induced a significant and cumulative reduction of beta band activity that correlated with a significant improvement of motor function.


CONCLUSIONS
These results highlight the potential effects of coordinated reset neuromodulation of the STN in PD patients and encourage further development of this approach as an alternative to conventional high-frequency deep brain stimulation in PD.
A phase 1 study of everolimus plus docetaxel plus cisplatin as induction chemotherapy for patients with locally and/or regionally advanced head and neck cancer.

BACKGROUND
Activation of the phosphatidylinositol-3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway is common in head and neck cancers, and it has been demonstrated that inhibition of mTOR complex 1 sensitizes cell lines to platinum and taxane chemotherapy. The authors conducted a phase 1 study to evaluate the addition of oral everolimus to cisplatin and docetaxel as induction chemotherapy for head and neck cancer.


METHODS
In this single-institution phase 1 study, 3 doses of daily everolimus were explored: 5 mg daily, 7.5 mg daily (administered as 5 mg daily alternating with 10 mg daily), and 10 mg daily of each 21-day cycle. Cisplatin and docetaxel doses were fixed (both were 75 mg/m(2) on day 1 of 21-day cycle) at each dose level with pegfilgrastim support. A standard 3 + 3 dose-escalation plan was used. After induction, patients were removed from protocol.


RESULTS
Eighteen patients were enrolled (15 men, 3 women), and their median Karnofsky performance status was 90. The most common toxicities were hyperglycemia, low hemoglobin, fatigue, and thrombocytopenia. Dose-limiting toxicities (DLTs) were neutropenic fever (1 event at dose level 2, 2 events at dose level 3), and all patients recovered fully from these DLTs. The maximum tolerated dose was exceeded at dose level 3. The progression-free survival rate at 1 year was 87.5% (95% confidence interval, 56.8%-96.7%); and, at 2 years, it was 76.6% (95% confidence interval, 41.2%-92.3%). Activating PI3K catalytic subunit α (PIK3CA) gene mutations were identified in 2 human papillomavirus-associated oropharyngeal cancers.


CONCLUSIONS
The phase 2 recommended dose was 7.5 mg daily for everolimus plus cisplatin and docetaxel (both at 75 mg/m(2) on day 1 of a 21-day cycle) given with pegfilgrastim support.
Socioeconomic status and COPD among low- and middle-income countries

BACKGROUND
Socioeconomic status (SES) is a strong social determinant of health. There remains a limited understanding of the association between SES and COPD prevalence among low- and middle-income countries where the majority of COPD-related morbidity and mortality occurs. We examined the association between SES and COPD prevalence using data collected in Argentina, Bangladesh, Chile, Peru, and Uruguay.


METHODS
We compiled lung function, demographic, and SES data from three population-based studies for 11,042 participants aged 35-95 years. We used multivariable alternating logistic regressions to study the association between COPD prevalence and SES indicators adjusted for age, sex, self-reported daily smoking, and biomass fuel smoke exposure. Principal component analysis was performed on monthly household income, household size, and education to create a composite SES index.


RESULTS
Overall COPD prevalence was 9.2%, ranging from 1.7% to 15.4% across sites. The adjusted odds ratio of having COPD was lower for people who completed secondary school (odds ratio [OR] =0.73, 95% CI 0.55-0.98) and lower with higher monthly household income (OR =0.96 per category, 95% CI 0.93-0.99). When combining SES factors into a composite index, we found that the odds of having COPD was greater with lower SES (interquartile OR =1.23, 95% CI 1.05-1.43) even after controlling for subject-specific factors and environmental exposures.


CONCLUSION
In this analysis of multiple population-based studies, lower education, lower household income, and lower composite SES index were associated with COPD. Since household income may be underestimated in population studies, adding household size and education into a composite index may provide a better surrogate for SES.
Color laser printer identification by analyzing statistical features on discrete wavelet transform

Color laser printers are nowadays abused to print or forge official documents and bills. Identifying color laser printers will be a step for media forensics. This paper presents a new method to identify color laser printers with printed color images. First, 39 noise features of color printed images are extracted from the statistical analysis of the HH sub-band on discrete wavelet transform. Then, these features are applied to train and classify the support vector machine for identifying the color laser printer. In the experiment, 9 models of 4 brands, Xerox, Konica, HP, Canon, are tested to classify the brand of color laser printer, the color toner, and the model of color laser printer. The results prove that the presented identification method performs well using the noise features of color printed images.
Continuous Learning of Human Activity Models Using Deep Nets

 Activity recognition strategies assume large amounts of labeled training data which require tedious human labor to label.  They also use hand engineered features, which are not best for all applications, hence required to be done separately for each application.  Several recognition strategies have benefited from deep learning for unsupervised feature selection, which has two important property – fine tuning and incremental update. Question! Can deep learning be leveraged upon for continuous learning of activity models from streaming videos? Contributions
Monte-Carlo tree search and rapid action value estimation in computer Go

Article history: Received 27 October 2010 Received in revised form 22 March 2011 Accepted 30 March 2011 Available online 6 April 2011
Bernini’s S. Andrea al Quirinale and Early Modern Architectural Representation

My research project focuses on Gianlorenzo Bernini's S. Andrea al Quirinale (1658-71), Rome, church of the Jesuit novitiate and largely underwritten by Prince Camillo Pamphili. This is not, however, a monographic study. S. Andrea is a vehicle for assessing fundamental and influential themes in early modern architectural representation as well as challenging several longstanding assumptions in current methodological approaches. The church is a milestone in any history of early modern architecture and a staple on most survey courses of western art. Over the last thirty years scholars have demonstrated that it was not built to an initial, unitary design but is instead the residue of protracted adaptation and revision (Connors, Frommel, Marder, Terhalle); elucidated the mechanisms of patronage; and explained its iconography (Cather, Careri, Levine). Yet, a full and coherent analysis of the intellectual priorities behind its formal choices, general and particular, is lacking. Indeed, as things stand, it is difficult to understand why Bernini himself considered S. Andrea his best work. The basic understanding probably remains that of a pioneering apologist of Baroque architecture, Rudolf Wittkower. Wittkower essentially characterized S. Andrea as a centrifuge, powered by an " overflowing vitality " that would burst the church apart were it not gripped and anchored by strategic architectural components. Wittkower's larger point was that, in Bernini's hands, the religious interior had ceased to be the formerly neutral vessel for mediation between man and God, and that a quiet and centripetal Renaissance had been substituted by an expressive and centrifugal Baroque. As this " dynamic " fallacy remains such a mental habit of virtually all analyses of early modern architecture, even at the level of simple metaphor, its conceptual genealogy deserves thorough historiographical investigation. For any such notion is completely absent from early modern thought and certainly any writings on architecture, whether treatise or anecdote. Dynamism, formal or spatial, is in fact a retrospective projection of modernist expectations onto early modern architecture. Ascribing motion to its undulating forms can be traced back to Jacob Burckhardt; equating this perceived motion with emotion, however, was the product of a late nineteenth-century aesthetic of empathy (influenced by the physiological theories of Johannes Volkeit and others) that matched the purported energy of the architecture with the supposed psychological state of the maker, as well as ascribing an animism to the buildings that haptically matched the (e)motions of the beholder. In architectural history this theory of design …
New Extendable Single-Stage Multi-input DC–DC/AC Boost Converter

This paper presents a new extendable single-stage multi-input dc-dc/ac boost converter. The proposed structure comprises of two bidirectional ports in the converter's central part to interface output load and battery storage, and several unidirectional input ports to get powers from different input dc sources. In fact, the proposed topology consists of two sets of parallel dc-dc boost converters, which are actively controlled to produce two independent output voltage components. Choosing two pure dc or two dc-biased sinusoidal values as the converter reference voltages, situations of the converter operating in two dc-dc and dc-ac modes are provided, respectively. The proposed converter utilizes minimum number of power switches and is able to step up the low-level input dc voltages into a high-level output dc or ac voltage without needing any output filter. The converter control system includes several current regulator loops for input dc sources and two voltage regulator loops for generating the desired output voltage components, resulting in autonomously charging/discharging the battery to balance the power flow. Due to the converter inherent multi-input multioutput control system, the small signal model of the converter is extracted and then the pole-placement control strategy via integral state feedback is applied for achieving the converter control laws. The validity and effectiveness of the proposed converter and its control performance are verified by simulation and experimental results.
Test-retest reliability of selected items of Health Behaviour in School-aged Children (HBSC) survey questionnaire in Beijing, China

BACKGROUND
Children's health and health behaviour are essential for their development and it is important to obtain abundant and accurate information to understand young people's health and health behaviour. The Health Behaviour in School-aged Children (HBSC) study is among the first large-scale international surveys on adolescent health through self-report questionnaires. So far, more than 40 countries in Europe and North America have been involved in the HBSC study. The purpose of this study is to assess the test-retest reliability of selected items in the Chinese version of the HBSC survey questionnaire in a sample of adolescents in Beijing, China.


METHODS
A sample of 95 male and female students aged 11 or 15 years old participated in a test and retest with a three weeks interval. Student Identity numbers of respondents were utilized to permit matching of test-retest questionnaires. 23 items concerning physical activity, sedentary behaviour, sleep and substance use were evaluated by using the percentage of response shifts and the single measure Intraclass Correlation Coefficients (ICC) with 95% confidence interval (CI) for all respondents and stratified by gender and age. Items on substance use were only evaluated for school children aged 15 years old.


RESULTS
The percentage of no response shift between test and retest varied from 32% for the item on computer use at weekends to 92% for the three items on smoking. Of all the 23 items evaluated, 6 items (26%) showed a moderate reliability, 12 items (52%) displayed a substantial reliability and 4 items (17%) indicated almost perfect reliability. No gender and age group difference of the test-retest reliability was found except for a few items on sedentary behaviour.


CONCLUSIONS
The overall findings of this study suggest that most selected indicators in the HBSC survey questionnaire have satisfactory test-retest reliability for the students in Beijing. Further test-retest studies in a large and diverse sample, as well as validity studies, should be considered for the future Chinese HBSC study.
Utility of fluorescence in situ hybridization as a non-invasive technique in the diagnosis of upper urinary tract urothelial carcinoma.

OBJECTIVES
To assess the clinical utility of a fluorescence in situ hybridization (FISH) assay as a non-invasive method for diagnosing and monitoring urothelial carcinoma (UC) in the upper urinary tract (UUT).


METHODS
Urine specimens from 30 consecutive patients with UUT UC and 19 healthy controls were analyzed by means of cytology and FISH. For FISH analysis, labelled probes to chromosomes 3, 7, 9, and 17 were used to assess chromosomal abnormalities indicative of malignancy. Sensitivity and specificity of both techniques were determined and compared. The frequency of chromosomal aberrations of malignant cells from UUT was also determined.


RESULTS
Overall sensitivity for FISH was significantly higher than the corresponding value for urine cytology (76.7% vs. 36%, respectively, p=0.0056). Specificities for FISH and cytology were 94.7% and 100%, respectively (p=ns). The positive and negative predictive values for FISH were 95.8% and 72%, whereas for cytology they were 100% and 54%, respectively. Of the genetically altered nuclei counted, 67%, 54%, and 43% presented polysomy in chromosomes 3, 7, and 17, respectively, and 21% presented a homozygous deletion of chromosome 9.


CONCLUSIONS
FISH assay of chromosomes 3, 7, 9, and 17 performed on exfoliated cells from voided urine specimens has greater sensitivity than cytology for detecting UUT UC whilst maintaining a similar specificity. The non-invasive nature of this method and its higher sensitivity could contribute to improving the current diagnosis of UUT UC.
Theoretical model of the grasp with vacuum gripper

Vacuum grippers are often notably diffused for grasping and moving very large and heavy objects. The absence of theoretical models able to foresee the behavior of the suction cup notably limits the applications and development of vacuum grippers. In this work, a study of grasping with a vacuum gripper has been carried out. A mathematical model is proposed for determining the forces of contact between suction cup and object. The principal purpose is to determine the minimum value of the static friction coefficient and the vacuum level in order to guarantee a firm grasp of the object during the movement, or rather without detachment or slipping of the suction cup. Finally, an example of the motion of an object grasped with suction cup is reported. 2006 Elsevier Ltd. All rights reserved.
The development and first validation of the Manchester Early Morning Symptoms Index (MEMSI) for patients with COPD.

AIM
Early morning symptoms (EMS) in people with COPD are associated with poor health, impaired activities and increased exacerbation risk. We describe the development and preliminary validation of the Manchester Early Morning Symptom Index (MEMSI) to quantify EMS in COPD.


METHODS
Focus groups and cognitive debriefing with patients with COPD were used to develop the potential item list, followed by a cross-sectional study to finalise the items for inclusion. In addition to test-retest reliability, comparisons with the St George's Respiratory Questionnaire-C (SGRQ-C), modified Medical Research Council Dyspnoea Scale, Functional Assessment of Chronic Illness Therapy Fatigue Scale (FACIT-F) and Hospital Anxiety and Depression Scale (HADS) evaluated construct validity. Hierarchical methods informed item deletion and Rasch analysis was applied to assess scale unidimensionality.


RESULTS
23 items were identified from the focus groups and debriefings. The cross-sectional study involved 203 patients with COPD (mean age 64.7 SD 7.5 years, male 63%, Global Initiative for Chronic Obstructive Lung Disease (GOLD): 1:14% 2:41% 3:25% 4: 7%). 13 items were removed during item reduction. MEMSI contains 10 items, demonstrates good overall fit to the Rasch model (χ(2) p=0.26) and item score distribution; excellent reliability (Person Separation Index: 0.91) and good test-retest repeatability (r=0.82). It correlates with the SGRQ-C (r=0.73), FACIT-F (r=-0.65) and HADS (r=0.53-0.54) indicating good construct validity.


CONCLUSIONS
MEMSI is a reliable and valid unidimensional measure of EMS for patients with COPD. It is simple to use and score supporting its suitability for research and clinical use. Work is underway to determine the minimal clinical important difference and cross-cultural validity.
Who's in Charge? An Empirical Study of Executive Staffing Practices in Foreign Subsidiaries

interests lie in the area of headquarters-subsidiary relationships, international human resource management and cross-cultural management. Abstract This study investigates executive staffing practices in foreign subsidiaries of multinational corporations. Grounded in a literature review of the reasons for employing either parent country nationals or host country nationals in top management positions in foreign subsidiaries, a number of factors influencing the choice between these alternatives are identified. Using a combination of an archival and mail survey research method, the influence of each of these factors is empirically tested with a sample of nearly 3000 observations.
Adjustment to the dissolution of a romantic relationship: effects of ex-relationship specific thought content valence

The purpose of this research was to examine the immediate effects of engaging in predominantly positively or predominantly negatively valenced thinking about one’s most recent romantic ex-relationship and assess whether these effects are unique from thinking about memories from a non-romantic relationship. The application of self-regulation theory within the context of rumination and romantic relationship breakups suggests that recalling positive memories from a relationship may make it more difficult to move on from the relationship that ended, whereas recalling negative memories may make moving on easier. Participants were instructed to write about a relationship memory, with experimental manipulations of the memory valence (positive vs. negative) and relationship type (exrelationship vs. friendship). Differences in outcome measures associated with adaptive and adverse breakup adjustment were subsequently examined. It was predicted that negatively valenced writing would yield higher ratings of adaptive adjustment measures and lower scores of adverse adjustment measures among participants in the ex-relationship condition, but yield lower scores of adaptive adjustment and higher scores on adverse adjustment among participants in the friendship condition. Results partially supported the hypotheses; participant ratings of adaptive outcomes were higher in the negative ex-relationship condition relative to the positive ex-relationship condition, and participants in the positive friendship condition higher ratings compared to those in the negative friendship condition. No meaningful differences were found with regard to adverse outcomes.