LLukas22/scidocs huggingface dataset:
Structure and dynamics of supercoil-stabilized DNA cruciforms.

Understanding DNA function requires knowledge of the structure of local, sequence-dependent conformations that can be dramatically different from the B-form helix. One alternative DNA conformation is the cruciform, which has been shown to have a critical role in the initiation of DNA replication and the regulation of transcription in certain systems. In addition, cruciforms provide a model system for structural studies of Holliday junctions, intermediates in homologous DNA recombination. Cruciforms are not thermodynamically stable in linear DNA due to branch point migration, which makes their study using many biophysical techniques problematic. Atomic Force Microscopy (AFM) was applied to visualize cruciforms in negatively supercoiled plasmid DNA. Cruciforms are seen as clear-cut extrusions on the DNA filament with the lengths of the arms consistent with the size of the hairpins expected from a 106 bp inverted repeat. The cruciform exists in two different conformations, an extended one with the angle of ca. 180 degrees between the hairpin arms and a compact, X-type conformation, with acute angles between the hairpin arms and the main DNA strands. The ratio of molecules with the different conformations of cruciforms depends on ionic conditions. In the presence of high salt or Mg cations, a compact, X-type conformation is highly preferable. Remarkably, the X-conformation was highly mobile allowing the cruciform arms to adopt a parallel orientation. The structure observed is consistent with a model of the Holliday junction with a parallel orientation of the exchanging strands.
Detection of Escherichia coli O157:H7 in soil and water using multiplex PCR.

AIMS
To evaluate the suitability of a multiplex PCR-based assay for sensitive and rapid detection of Escherichia coli O157:H7 in soil and water.


METHODS AND RESULTS
Soil and water samples were spiked with E. coli O157:H7 and subjected to two stages of enrichment prior to multiplex PCR. Detection sensitivities were as high as 1 cfu ml(-1) drinking water and 2 cfu g(-1) soil. Starvation of E. coli O157:H7 for 35 d prior to addition to soil did not affect the ability of the assay to detect initial cell numbers as low as 10 cfu g(-1) soil. Use of an 8-h primary enrichment enabled detection of as few as 6 cfu g(-1) soil, and 10(4) cfu g(-1) soil with a 6-h primary enrichment. When soil was inoculated with 10(5) cfu g(-1), the PCR assay indicated persistence of E. coli O157:H7 during a 35 d incubation. However, when soil was inoculated with lower numbers of pathogen, PCR amplification signals indicated survival to be dependent on cell concentration.


CONCLUSIONS
A multiplex PCR-based assay, in combination with an enrichment strategy enabled sensitive and rapid detection of E. coli O157:H7 in soil and water.


SIGNIFICANCE AND IMPACT OF THE STUDY
The ability to sensitively detect E.coli O157:H7 in environmental material within one working day represents a considerable advancement over alternative more time-consuming methods for detection of this pathogen.
Resistance exercise, disability, and pain catastrophizing in obese adults with back pain.

PURPOSE
The purpose of this study was to compare the effects of two different resistance exercise protocols on self-reported disability, fear avoidance beliefs, pain catastrophizing, and back pain symptoms in obese, older adults with low back pain (LBP).


METHODS
Obese adults (n = 49, 60-85 yr) with chronic LBP were randomized into a total body resistance exercise intervention (TOTRX), lumbar extensor exercise intervention (LEXT), or a control group (CON). Main outcomes included perceived disability (Oswestry Disability Index, Roland Morris Disability Questionnaire). Psychosocial measures included the Fear Avoidance Beliefs survey, Tampa Scale of Kinesiophobia, and Pain Catastrophizing Scale. LBP severity was measured during three functional tasks: walking, stair climbing, and chair rise using an 11-point numerical pain rating scale.


RESULTS
The TOTRX group had greater reductions in self-reported disability scores due to back pain (Oswestry Disability Index, Roland Morris Disability Questionnaire) compared with those in the LEXT (P < 0.05). The Pain Catastrophizing Scale scores decreased in the TOTRX group compared with that in the CON group by month 4 (64.3% vs 4.8%, P < 0.05). Pain severity during chair rise activity and walking was decreased in both the LEXT and TOTRX groups relative to the CON group.


CONCLUSIONS
Greater reductions in perceived disability due to LBP can be achieved with TOTRX compared with those achieved with LEXT. Pain catastrophizing and pain severity decreased most with TOTRX. The positive change in psychological outlook may assist obese, older adults with chronic back pain in reconsidering the harmfulness of the pain and facilitate regular participation in other exercise programs.
BFQA: A Bengali Factoid Question Answering System

Question Answering (QA) research for factoid questions has recently achieved great success. Presently, QA systems developed for European, Middle Eastern and Asian languages are capable of providing answers with reasonable accuracy. However, Bengali being among themost spoken languages in theworld, no factoid question answering system is available for Bengali till date. This paper describes the first attempt on building a factoid question answering system for Bengali language. The challenges in developing a question answering system for Bengali have been discussed. Extraction and ranking of relevant sentences have also been proposed. Also extraction strategy of the ranked answers from the relevant sentences are suggested for Bengali question answering system.
Mining novelty-seeking trait across heterogeneous domains

An incisive understanding of personal psychological traits is not only essential to many scientific disciplines, but also has a profound business impact on online recommendation. Recent studies in psychology suggest that novelty-seeking trait is highly related to consumer behavior. In this paper, we focus on understanding individual novelty-seeking trait embodied at different levels and across heterogeneous domains. Unlike the questionnaire-based methods widely adopted in the past, we first present a computational framework, Novel Seeking Model (NSM), for exploring the novelty-seeking trait implied by observable activities. Then, we explore the novelty-seeking trait in two heterogeneous domains: check-in behavior in location based social networks, which reflects mobility patterns in the physical world, and online shopping behavior on e-commerce sites, which reflects consumption concepts in economic activities. To demonstrate the effectiveness of NSM, we conducted extensive experiments, with a large dataset covering the two-domain activities for hundreds of thousands of individuals. Our results suggest that NSM offers a powerful paradigm for 1) presenting an effective measurement of a personality trait that can explicitly explain the deviation of individuals from the habits of individuals and crowds; 2) uncovering the correlation of novelty-seeking trait at different levels and across heterogeneous domains. The proposed method provides emerging implications for personalized cross-domain recommendation and targeted advertising.
Mode of allocation and social demographic factors correlate with impaired quality of life after liver transplantation

BACKGROUND
Health-related Quality of life (HRQoL) is a major goal of clinical management after liver transplantation (LTx). There is still disagreement on the effects of social-demographic factors and changes in the allocation system on HRQoL. The aim of this study was to evaluate the impact of social-demographic factors, mode of organ-allocation, waiting time and hepatocellular carcinoma (HCC) on HRQoL after LTx.


METHODS
HRQoL was assessed using the EORTC-QLQ-C30 questionnaire, which was sent to 238 recipients. Investigated parameters included age, sex, distance to transplant center, follow-up at hospital, size of hometown, highest education, marital status, having children, background liver disease, waiting time, mode of allocation, HCC, hospitalization after LTx and diagnosis of malignancy after LTx. All evaluated parameters were entered into multivariate linear regression analysis.


RESULTS
Completed questionnaire were returned by 73% of the recipients. After LTx, the HRQoL-function scales increased over time. Age, marital status, highest education, completed professional training, working status, job position, duration of waiting time to LTx, distance to transplant center, place offollow, HU-statuts, mode of organ allocation and duration of hospitalization were associated with significantly worse function- and significantly lower symptom scales. HCC as a primary disease did not affect HRQoL.


CONCLUSIONS
Low HRQoL correlated significantly with MELD-based organ allocation, more than 28-day hospitalization, divorced status, lower education- and non-working status, higher distance to transplant center, follow up at transplant center, HU-status, shorter waiting time to LTx and younger age. Improvement of HRQoL after LTx may require clinical management of pain, psychotherapy and financial support.
mHealth Education Applications Along the Cancer Continuum

The majority of adults worldwide own a mobile phone, including those in under-resourced communities. Mobile health (mhealth) education technologies present a promising mechanism for improving cancer prevention, treatment, and follow-up. The purpose of this study was to summarize the literature related to mobile phone (mhealth) applications for patient education specific to cancer and identify current recommendations from randomized studies. In particular, we were interested in identifying mobile phone applications along the cancer continuum, from cancer prevention to survivorship. The authors identified 28 articles reporting on mobile applications for patients related to cancer. Articles were identified in all categories along the cancer continuum, including health professional involvement in application development. Of these, six involved direct patient education, and eight focused on improving patient/professional communication and patient self-management. However, only six of the studies were randomized interventions. The potential for mobile applications to help overcome the “health care gap” has not yet been realized in the studies from the USA that were reviewed for this paper. However, early recommendations are emerging that support the use of mHealth communications to change behaviors for cancer prevention, early detection, and symptom management and improved patient-provider communication. Recommendations include short messages, use of multiple modalities as patient characteristics dictate comfort with mHealth communication, and the inclusion of patients and health professionals to develop and test applications. Tailoring mHealth to particular cultures, languages, and ethnic groups may also represent a unique possibility to provide accessible information and education at minimal cost for under-resourced communities and individuals.
No hope without compassion: the importance of compassion in recovery-focused mental health services.

BACKGROUND
Whilst current policy is replete with recovery language and references to the need for services to create a sense of hope and optimism, there is less understanding about how such hope may be engendered within services. We propose that an understanding of compassion is necessary to appreciate what actually stimulates hope-inspiring practices.


AIMS
An examination of the continuing relevance of compassion to mental health care and an exploration of its place within modern mental health policy and practice.


METHODS
A review of the compassion deficit in mental health care and a critical examination of whether the direction of current mental health policy in the UK is likely to facilitate compassionate care.


RESULTS
Compassion needs to be viewed not merely as an individual expression or property but something which must be nurtured in context, through relationships, cultures and healing environments. However, current mental health policy and practice does not appear to prioritise the development of such contexts.


CONCLUSION
Attention to fostering compassion would help to shift the language of "recovery" (or "well-being") beyond the twin dangers of rhetoric and/or imposing preconceived definitions, models or expectations of what recovery "should" be. Therefore, the development of compassionate contexts should have a stronger place in modern mental health practice and policy.
Abbreviated HIV counselling and testing and enhanced referral to care in Uganda: a factorial randomised controlled trial

BACKGROUND
HIV counselling and testing and linkage to care are crucial for successful HIV prevention and treatment. Abbreviated counselling could save time; however, its effect on HIV risk is uncertain and methods to improve linkage to care have not been studied.


METHODS
We did this factorial randomised controlled study at Mulago Hospital, Uganda. Participants were randomly assigned to abbreviated or traditional HIV counselling and testing; HIV-infected patients were randomly assigned to enhanced linkage to care or standard linkage to care. All study personnel except counsellors and the data officer were masked to study group assignment. Participants had structured interviews, given once every 3 months. We compared sexual risk behaviour by counselling strategy with a 6·5% non-inferiority margin. We used Cox proportional hazards analyses to compare HIV outcomes by linkage to care over 1 year and tested for interaction by sex. This trial is registered with ClinicalTrials.gov (NCT00648232).


FINDINGS
We enrolled 3415 participants; 1707 assigned to abbreviated counselling versus 1708 assigned to traditional. Unprotected sex with an HIV discordant or status unknown partner was similar in each group (232/823 [27·9%] vs 251/890 [28·2%], difference -0·3%, one-sided 95% CI 3·2). Loss to follow-up was lower for traditional counselling than for abbreviated counselling (adjusted hazard ratio [HR] 0·61, 95% CI 0·44-0·83). 1003 HIV-positive participants were assigned to enhanced linkage (n=504) or standard linkage to care (n=499). Linkage to care did not have a significant effect on mortality or receipt of co-trimoxazole. Time to treatment in men with CD4 cell counts of 250 cells per μL or fewer was lower for enhanced linkage versus standard linkage (adjusted HR 0·60, 95% CI 0·41-0·87) and time to HIV care was decreased among women (0·80, 0·66-0·96).


INTERPRETATION
Abbreviated HIV counselling and testing did not adversely affect risk behaviour. Linkage to care interventions might decrease time to enrolment in HIV care and antiretroviral treatment and thus might affect secondary HIV transmission and improve treatment outcomes.


FUNDING
US National Institute of Mental Health.
Inland Wetland Definitions

. . . . . . . . . . . . . . . Introduction. .............. Aspects of Definitions of Inland Wetlands Specialized Fields of Study ...... Geology and Hydrogeology ...... Pedology .............. Biology. . . . . . . . . . . . . . .. Higher Plants .......... Lower Plants .......... Zoology . . . . . . . . . . . . . Systems Ecology ......... Economics .............. Summary of Definitions. Proposed Inland Wetland Definition for Connecticut Appendices ................... I. Descriptions and Explanations of Terms . II. Hydrological Model of Wetlands ..... III. Participants .............. vi
The Diversity of Biosimilar Design and Development: Implications for Policies and Stakeholders

Biosimilars are required to be similar or highly similar in structure to their biologic reference product but are neither expected nor required to contain identical active substances. For example, glycosylated biosimilars approved to date demonstrate quantitative and qualitative structural differences from their reference product and exemplify the latitude of variations permitted for biosimilars. Although differences between a candidate biosimilar and its reference product will be evaluated for differential clinical effects during biosimilarity assessment, it is unlikely that potential differences between any two indirectly related biosimilars will be formally evaluated. Furthermore, biosimilar pathways permit variations in pharmaceutical attributes, clinical development approaches, and regulatory outcomes, resulting in further diversity of attributes among approved biosimilars. Because biosimilars may vary across the ranges of structural and functional acceptance criteria, they should not be treated like multisource, generic drugs.
Single-impurity-induced Dicke quantum phase transition in a cavity-Bose-Einstein condensate

We present a new generalized Dicke model, an impurity-doped Dicke model (IDDM), by the use of an impurity-doped cavity-Bose-Einstein condensate (BEC). It is shown that the impurity atom can induce Dicke quantum phase transition (QPT) from the normal phase to superradiant phase at a critic value of the impurity population. It is found that the impurity-induced Dicke QPT can happen in an arbitrary field-atom coupling regime while the Dicke QPT in the standard Dicke model occurs only in the strong coupling regime of the cavity field and atoms. This opens the possibility to realize the control of quantum properties of a macroscopic-quantum system (BEC) by using a microscopic quantum system (a single impurity atom).
Deep crustal reflectors under Reydarfjördur, eastern Iceland:crustal accretion above the Iceland mantle plume

Summary 
 
Deep seismic reflection profiling on the Faroe–Iceland Ridge Experiment (FIRE) imaged a sequence of dipping events in the upper to |-crust beneath the Tertiary lava pile in Reydarfjordur, eastern Iceland. These events dip towards the spreading centre at which the crust was formed, and continue down to ∼ 6 s two-way time, corresponding to depths down to 15–18 km. Similar crustal reflections have been observed previously within the crust in other areas of Iceland, although the reflective events located by previous surveys have not been interpreted rigorously. In this study we calculate synthetic seismograms from modelled sequences of lava flows to examine the reflective character of a lava πle. The synthesized lava pile sections are based on field measurements made in the Reydarfjordur area: the 1 km vertical exposures on the sides of the fjord are composed of lava flows within stratigraphic units which have a range of compositions, and some intercalated tuffaceous clastic horizons. 
 
 
 
We compare the synthetic seismograms with our seismic reflection data to test the interpretation that the deep dipping reflections are caused by a gently dipping sequence of subaerially erupted lavas. We conclude that the upper and mid-crustal reflections that we observe can be interpreted as lava flow sequences similar to those seen at the surface, with the main reflections resulting from packets of flows of similar thicknesses. The reflectors that we have imaged beneath Iceland are similar to those defining the seaward-dipping reflectors on the volcanic continental margins, and we therefore suggest that the seaward-dipping reflections commonly result from packets of lavas with similar distributions of thicknesses. 
 
 
 
The occurrence of lavas down to 15–18 km beneath Reydarfjordur can be explained partly by multiple episodes of accretion of the upper crust, although the volcanic processes forming the crust in Iceland generally lead to advection of extrusive material to mid-crustal levels. The production of an average extrusive layer totalling 15 km thickness is within reasonable estimates of the current volcanic productivity. The advection of frozen lava flows to mid-crustal levels contributes to the maintenance of the subsolidus crust that is observed on Iceland, and the zeolite minerals within the extrusive sequence may be responsible for the crustal low resistivity zone that has been observed using magnetotelluric techniques.
Treatment of rheumatoid arthritis with roxithromycin: a randomized trial.

BACKGROUND
High levels of antibodies to oral anaerobic bacteria have been found in the serum and synovial fluid of patients with rheumatoid arthritis (RA). Macrolide antibiotics are active against oral anaerobic bacteria. The aim of this trial was to evaluate the efficacy of roxithromycin in patients with RA who had not responded to disease-modifying antirheumatic drugs.


METHODS
This was a 6-month, randomized, double-blind, placebo-controlled trial. We treated 100 patients with active RA with either once-daily oral roxithromycin 300 mg or daily oral placebo for 6 months. The primary efficacy variable was the percentage of patients who had a 20% improvement according to the American College of Rheumatology (ACR) criteria (an ACR20 response) at 6 months. Secondary outcome measures were 50% improvement and 70% improvement according to ACR criteria (an ACR50 response and an ACR70 response, respectively).


RESULTS
A significantly greater percentage of patients treated with roxithromycin 300 mg met the ACR 20% improvement criteria (ie, achieved an ACR20 response) at 6 months compared with patients who received placebo (60% vs 34%; P = 0.009). Greater percentages of patients treated with roxithromycin 300 mg also achieved ACR50 responses (38% vs 12%; P = 0.003) and ACR70 responses (18% vs 2%; P = 0.008) compared with patients who received placebo. Roxithromycin was well tolerated, with an overall safety profile similar to that of placebo.


CONCLUSION
In patients with active RA, treatment with roxithromycin significantly improved the signs and symptoms of RA.