LLukas22/scidocs huggingface dataset:
Leptospirosis in pigs, dogs, rodents, humans, and water in an area of the Colombian tropics

Leptospirosis is a reemerging zoonosis of global distribution and is one of the causes of hemorrhagic fevers in the tropics. We sought to determine seroprevalence in humans and animals and isolate Leptospira interrogans sensu lato in domestic animals, rodents, and water sources. The study was conducted in a tropical area of the middle Sinú in Cordoba, Colombia. In a prospective descriptive study, we collected blood and urine from pigs and dogs, sera from rural human workers, sera and kidney macerates of rodents, and water samples from environmental sources. We used microagglutination to screen for antibodies to 13 serovars. Strains were cultured on the Ellinghausen–McCullough–Johnson–Harris medium and confirmed by PCR amplifying lipL32 gene. Seroprevalence was 55.9 % in pigs, 35.2 % in dogs, and 75.8 % in humans; no antibody was detected, and no Leptospira were isolated from kidney macerates of rodents. Seven L. interrogans sensu lato strains were isolated: three from pigs, two from dogs, and two from water. High seroprevalence in pigs, dogs, and humans, concomitant to isolation of strains, demonstrates that in Cordoba, transmission exists among animals, the environment, and humans, which warrants the implementation of public health intervention measures to reduce the epidemiological impact of leptospirosis in the region.
The reasons for triple therapy in stable COPD patients in Japanese clinical practice

BACKGROUND
Triple combination therapy involving long-acting muscarinic antagonists long-acting β2 agonists, and inhaled corticosteroids has recently become an option for maintenance treatment of COPD. Some add-on clinical trials have reported the benefits of these combinations. However, the process to step up to triple therapy varies for individual cases.


METHODS
Keio University and affiliated hospitals conducted an observational COPD cohort study, recruiting patients diagnosed as having COPD by pulmonary physicians and those referred for investigation of possible COPD. Their prescription history and clinical course were retrospectively analyzed based on the physicians' medical records and patient questionnaires. This study was registered with UMIN (UMIN000003470, April 10, 2010).


RESULTS
A total of 95 of the 445 COPD patients (21%) were treated with inhaled corticosteroids/long-acting β2 agonists/long-acting muscarinic antagonists as maintenance therapy, including 12 in COPD Grade I, 31 in Grade II, 38 in Grade III, and 14 in Grade IV, based on the Global Initiative for Chronic Obstructive Lung Disease spirometric grading. For more than half of the patients on triple therapy, the treatment had been intensified due to unsatisfactory improvement of symptoms, and 32% were treated with triple therapy due to comorbid asthma. In contrast, there were COPD patients whose therapy was maintained after starting with triple therapy because of their serious conditions or concurrent exacerbation at diagnosis (8%).


CONCLUSION
Triple therapy was often prescribed in the real-life management of COPD, even in patients whose airflow limitation was not severe. To better control symptoms was the major reason for choosing triple therapy, regardless of the severity of COPD, in Japan.
Trivariate solid T-spline construction from boundary triangulations with arbitrary genus topology

A comprehensive scheme is described to construct rational trivariate solid T-splines from boundary triangulations with arbitrary topology. To extract the topology of the input geometry, we first compute a smooth harmonic scalar field defined over the mesh, and saddle points are extracted to determine the topology. By dealing with the saddle points, a polycube whose topology is equivalent to the input geometry is built, and it serves as the parametric domain for the trivariate T-spline. A polycube mapping is then used to build a one-to-one correspondence between the input triangulation and the polycube boundary. After that, we choose the deformed octree subdivision of the polycube as the initial T-mesh, and make it valid through pillowing, quality improvement and applying templates to handle extraordinary nodes and partial extraordinary nodes. The T-spline that is obtained is C2-continuous everywhere over the boundary surface except for the local region surrounding polycube corner nodes. The efficiency and robustness of the presented technique are demonstrated with several applications in isogeometric analysis. © 2012 Elsevier Ltd. All rights reserved.
Coherent optical orthogonal frequency division multiplexing

Introduction: Orthogonal frequency division multiplexing (OFDM) has been extensively investigated to combat RF microwave multipath fading, and has been widely implemented in various digital communication standards such as wireless local area network standards (WIFI IEEE 802.11a) [1]. In this Letter, we propose an optical equivalent of the RF OFDM called coherent optical OFDM (CO-OFDM) to combat dispersion in fibre media. We show that with CO-OFDM the optical-signal-to-noise ratio (OSNR) penalty can be maintained below 2 dB for 3000 km transmission through standard-singlemode fibre (SSMF) without chromatic dispersion compensation. As such, CO-OFDM may be an alternative solution for electrical predistortion [2], but with the additional advantage that the optical signal can be dropped at any point within 3000 km.
Alternative synthetic methods through new developments in catalysis by gold.

2.7. Hydroxylation Reactions of Allenes 3282 2.8. Hydroamination Reactions of Allenes 3284 2.9. Hydrothiolation of Allenes 3284 2.10. Hydroalxoxylation of Alkenes and 1,3-Dienes 3286 2.11. Hydroamination of Alkenes and 1,3-Dienes 3287 2.12. Hydrothiolation of Conjugated Olefins 3289 3. Activation of Carbonyl/Imine Groups and Alcohols 3289 3.1. Condensation Reactions 3289 3.2. Addition Reactions 3291 3.3. Aldol Reactions 3294 3.4. Hydroand Carbosilylation Reactions 3295 3.5. Nucleophilic Substitution Reactions of Alcohols 3297 4. Gold-Catalyzed C-H Bond Functionalization 3297 4.1. Csp3-H Bond Functionalization 3298 4.2. Csp2-H Bond Functionalization 3299 4.3. Csp-H Bond Functionalization 3304 5. Gold-Catalyzed Selective Reductions 3305 5.1. Catalytic Hydrogenation of Alkenes 3306 5.2. Selective Reductions of R, -Unsaturated Carbonyl Groups and 1,3-Dienes 3306
The interactive toxicity of cadmium, copper, and zinc to Ceriodaphnia dubia and rainbow trout (Oncorhynchus mykiss).

Traditionally, aquatic toxicity studies examine the toxicity of a single chemical to an organism. Organisms in nature, however, may be exposed to multiple toxicants. Given this is a more realistic exposure scenario in situ, the authors sought to understand the interactive toxicity of multiple metals to aquatic organisms. The authors performed a series of studies using equitoxic mixtures of cadmium, copper, and zinc to 2 aquatic organisms, rainbow trout (Oncorhynchus mykiss) and the waterflea, Ceriodaphnia dubia. Single metal toxicity tests were conducted to determine the acute median lethal concentration (LC50) values for O. mykiss and short-term, chronic median effective concentration (EC50) values for C. dubia. All 3 metals were then combined in equitoxic concentrations for subsequent mixture studies using a toxic unit (TU) approach (i.e., 1 TU = EC50 or LC50). For C. dubia, the mixture study showed greater-than-additive effects in hard water (TU-based EC50 = 0.74 TU), but less-than-additive effects in soft water (TU-based EC50 = 1.93 TU). The mixture effects for O. mykiss showed less-than-additive effects in both hard and soft waters, with TU-based LC50 values of 2.33 total TU and 2.22 total TU, respectively. These data are useful in helping understand metal mixture toxicity in aquatic systems and indicate that although in most situations the assumption of additivity of metal mixture toxicity is valid, under certain conditions it may not be sufficiently protective.
Use of the PiCCO system in critically ill patients with septic shock and acute respiratory distress syndrome: a study protocol for a randomized controlled trial

BACKGROUND
Hemodynamic monitoring is very important in critically ill patients with shock or acute respiratory distress syndrome(ARDS). The PiCCO (Pulse index Contour Continuous Cardiac Output, Pulsion Medical Systems, Germany) system has been developed and used in critical care settings for several years. However, its impact on clinical outcomes remains unknown.


METHODS/DESIGN
The study is a randomized controlled multi-center trial. A total of 708 patients with ARDS, septic shock or both will be included from January 2012 to January 2014. Subjects will be randomized to receive PiCCO monitoring or not. Our primary end point is 30-day mortality, and secondary outcome measures include ICU length of stay, days on mechanical ventilation, days of vasoactive agent support, ICU-free survival days during a 30-day period, mechanical-ventilation-free survival days during a 30-day period, and maximum SOFA score during the first 7 days.


DISCUSSION
We investigate whether the use of PiCCO monitoring will improve patient outcomes in critically ill patients with ARDS or septic shock. This will provide additional data on hemodynamic monitoring and help clinicians to make decisions on the use of PiCCO.


TRIAL REGISTRATION
http://www.clinicaltrials.gov NCT01526382.
Cultural differences in medical communication: a review of the literature.

OBJECTIVE
Culture and ethnicity have often been cited as barriers in establishing an effective and satisfying doctor-patient relationship. The aim of this paper is to gain more insight in intercultural medical communication difficulties by reviewing observational studies on intercultural doctor-patient communication. In addition, a research model for studying this topic in future research is proposed.


METHODS
A literature review using online databases (Pubmed, Psychlit) was performed.


RESULTS
Findings reveal major differences in doctor-patient communication as a consequence of patients' ethnic backgrounds. Doctors behave less affectively when interacting with ethnic minority patients compared to White patients. Ethnic minority patients themselves are also less verbally expressive; they seem to be less assertive and affective during the medical encounter than White patients.


CONCLUSION
Most reviewed studies did not relate communication behaviour to possible antecedent culture-related variables, nor did they assess the effect of cultural variations in doctor-patient communication on outcomes, leaving us in the dark about reasons for and consequences of differences in intercultural medical communication. Five key predictors of culture-related communication problems are identified in the literature: (1) cultural differences in explanatory models of health and illness; (2) differences in cultural values; (3) cultural differences in patients' preferences for doctor-patient relationships; (4) racism/perceptual biases; (5) linguistic barriers. It is concluded that by incorporating these variables into a research model future research on this topic can be enhanced, both from a theoretical and a methodological perspective.


PRACTICE IMPLICATIONS
Using a cultural sensitive approach in medical communication is recommended.
Development and Validation of the User Version of the Mobile Application Rating Scale (uMARS)

BACKGROUND
The Mobile Application Rating Scale (MARS) provides a reliable method to assess the quality of mobile health (mHealth) apps. However, training and expertise in mHealth and the relevant health field is required to administer it.


OBJECTIVE
This study describes the development and reliability testing of an end-user version of the MARS (uMARS).


METHODS
The MARS was simplified and piloted with 13 young people to create the uMARS. The internal consistency and test-retest reliability of the uMARS was then examined in a second sample of 164 young people participating in a randomized controlled trial of a mHealth app. App ratings were collected using the uMARS at 1-, 3,- and 6-month follow up.


RESULTS
The uMARS had excellent internal consistency (alpha = .90), with high individual alphas for all subscales. The total score and subscales had good test-retest reliability over both 1-2 months and 3 months.


CONCLUSIONS
The uMARS is a simple tool that can be reliably used by end-users to assess the quality of mHealth apps.
[Predictive factors of complications during CT-guided transthoracic biopsy].

INTRODUCTION
CT-guided transthoracic core-needle biopsy (TTNB) is frequently used for the diagnosis of lung nodules. The aim of this study is to describe TTNBs' complications and to investigate predictive factors of complications.


METHODS
All consecutive TTNBs performed in three centers between 2006 and 2012 were included. Binary logistic regression was used for multivariate analysis.


RESULTS
Overall, 970 TTNBs were performed in 929 patients. The complication rate was 34% (life-threatening complication in 6%). The most frequent complications were pneumothorax (29% included 4% which required chest-tube) and hemoptysis (5%). The mortality rate was 0.1% (n=1). In multivariate analysis, predictive factor for a complication was small target size (AOR=0.984; 95% CI [0.976-0.992]; P<0.001). This predictive factor was also found for occurrence of life-threatening complication (AOR=0.982; [0.965-0.999]; P=0.037), of pneumothorax (AOR=0.987; [0.978-0.995]; P=0.002) and of hemoptysis (AOR=0.973; [0.951-0.997]; P=0.024).


CONCLUSION
One complication occurred in one-third of TTNBs. The proportion of life-threatening complication was 6%. A small lesion size was predictive of complication occurrence.
An fMRI Study of Risky Decision Making: The Role of Mental Preparation and Conflict

INTRODUCTION
The current study aimed to elucidate the role of preparatory cognitive control in decision making and its neural correlates using functional Magnetic Resonance Imaging (fMRI). To this effect, by employing a series of new cognitive tasks, we assessed the role of preparatory cognitive control in monetary (risky) decision making.


METHODS
The participants had to decide between a risky and a safe gamble based on their chance of winning (high or low). In the 2-phase gambling task (similar to Cambridge gambling task), the chance and the gamble were presented at the same time (i.e. in a single phase), but in a new 3-phase gambling task, the chance is presented before the gamble. The tasks ended with a feedback phase.


RESULTS
In the 3-phase task, holding the chance in memory to guide their decision enabled the participants to have more control on their risk taking behaviors as shown by activation in a network of brain areas involved in the control and conflict, including dorsal Anterior Cingulate Cortex (dACC), indexed by faster reaction times and better performance in the gambling task, and the temporal lobe, which has a role in holding contextual information.


DISCUSSION
Holding information in memory to guide decision presumably enables the participants to have more control on their risk taking behaviors. The conflict and uncertainty resulting from this risky decision was indexed by the activation of dACC, known to be activated in conflict and cognitive control.
Classification of subtype of acute ischemic stroke. Definitions for use in a multicenter clinical trial. TOAST. Trial of Org 10172 in Acute Stroke Treatment.

BACKGROUND AND PURPOSE
The etiology of ischemic stroke affects prognosis, outcome, and management. Trials of therapies for patients with acute stroke should include measurements of responses as influenced by subtype of ischemic stroke. A system for categorization of subtypes of ischemic stroke mainly based on etiology has been developed for the Trial of Org 10172 in Acute Stroke Treatment (TOAST).


METHODS
A classification of subtypes was prepared using clinical features and the results of ancillary diagnostic studies. "Possible" and "probable" diagnoses can be made based on the physician's certainty of diagnosis. The usefulness and interrater agreement of the classification were tested by two neurologists who had not participated in the writing of the criteria. The neurologists independently used the TOAST classification system in their bedside evaluation of 20 patients, first based only on clinical features and then after reviewing the results of diagnostic tests.


RESULTS
The TOAST classification denotes five subtypes of ischemic stroke: 1) large-artery atherosclerosis, 2) cardioembolism, 3) small-vessel occlusion, 4) stroke of other determined etiology, and 5) stroke of undetermined etiology. Using this rating system, interphysician agreement was very high. The two physicians disagreed in only one patient. They were both able to reach a specific etiologic diagnosis in 11 patients, whereas the cause of stroke was not determined in nine.


CONCLUSIONS
The TOAST stroke subtype classification system is easy to use and has good interobserver agreement. This system should allow investigators to report responses to treatment among important subgroups of patients with ischemic stroke. Clinical trials testing treatments for acute ischemic stroke should include similar methods to diagnose subtypes of stroke.
Resource-oriented music therapy for psychiatric patients with low therapy motivation: Protocol for a randomised controlled trial [NCT00137189]

BACKGROUND
Previous research has shown positive effects of music therapy for people with schizophrenia and other mental disorders. In clinical practice, music therapy is often offered to psychiatric patients with low therapy motivation, but little research exists about this population. The aim of this study is to examine whether resource-oriented music therapy helps psychiatric patients with low therapy motivation to improve negative symptoms and other health-related outcomes. An additional aim of the study is to examine the mechanisms of change through music therapy.


METHODS
144 adults with a non-organic mental disorder (ICD-10: F1 to F6) who have low therapy motivation and a willingness to work with music will be randomly assigned to an experimental or a control condition. All participants will receive standard care, and the experimental group will in addition be offered biweekly sessions of music therapy over a period of three months. Outcomes will be measured by a blind assessor before and 1, 3, and 9 months after randomisation.


DISCUSSION
The findings to be expected from this study will fill an important gap in the knowledge of treatment effects for a patient group that does not easily benefit from treatment. The study's close link to clinical practice, as well as its size and comprehensiveness, will make its results well generalisable to clinical practice.
Effect of thalidomide on clinical remission in children and adolescents with refractory Crohn disease: a randomized clinical trial.

IMPORTANCE
Pediatric-onset Crohn disease is more aggressive than adult-onset disease, has high rates of resistance to existing drugs, and can lead to permanent impairments. Few trials have evaluated new drugs for refractory Crohn disease in children.


OBJECTIVE
To determine whether thalidomide is effective in inducing remission in refractory pediatric Crohn disease.


DESIGN, SETTING, AND PATIENTS
Multicenter, double-blind, placebo-controlled, randomized clinical trial of 56 children with active Crohn disease despite immunosuppressive treatment, conducted August 2008-September 2012 in 6 pediatric tertiary care centers in Italy.


INTERVENTIONS
Thalidomide, 1.5 to 2.5 mg/kg per day, or placebo once daily for 8 weeks. In an open-label extension, nonresponders to placebo received thalidomide for an additional 8 weeks. All responders continued to receive thalidomide for an additional minimum 52 weeks.


MAIN OUTCOMES AND MEASURES
Primary outcomes were clinical remission at week 8, measured by Pediatric Crohn Disease Activity Index (PCDAI) score and reduction in PCDAI by ≥25% or ≥75% at weeks 4 and 8. Primary outcomes during the open-label follow-up were clinical remission and 75% response.


RESULTS
Twenty-eight children were randomized to thalidomide and 26 to placebo. Clinical remission was achieved by significantly more children treated with thalidomide (13/28 [46.4%] vs 3/26 [11.5%]; risk ratio [RR], 4.0 [95% CI, 1.2-12.5]; P = .01; number needed to treat [NNT], 2.86). Responses were not different at 4 weeks, but greater improvement was observed at 8 weeks in the thalidomide group (75% response, 13/28 [46.4%] vs 3/26 [11.5%]; RR, 4.0 [95% CI, 1.2-12.5]; NNT = 2.86; P = .01; and 25% response, 18/28 [64.2%] vs 8/26 [30.8%]; RR, 2.1 [95% CI, 1.1-3.9]; NNT = 2.99; P = .01). Of the nonresponders to placebo who began receiving thalidomide, 11 of 21 (52.4%) subsequently reached remission at week 8 (RR, 4.5 [95% CI, 1.4-14.1]; NNT = 2.45; P = .01). Overall, 31 of 49 children treated with thalidomide (63.3%) achieved clinical remission, and 32 of 49 (65.3%) achieved 75% response. Mean duration of clinical remission in the thalidomide group was 181.1 weeks (95% CI, 144.53-217.76) vs 6.3 weeks (95% CI, 3.51-9.15) in the placebo group (P < .001). Cumulative incidence of severe adverse events was 2.1 per 1000 patient-weeks, with peripheral neuropathy the most frequent severe adverse event.


CONCLUSIONS AND RELEVANCE
In children and adolescents with refractory Crohn disease, thalidomide compared with placebo resulted in improved clinical remission at 8 weeks of treatment and longer-term maintenance of remission in an open-label follow-up. These findings require replication to definitively determine clinical utility of this treatment.


TRIAL REGISTRATION
clinicaltrials.gov Identifier: NCT00720538.
Climate change , sea-level rise , and conservation : keeping island biodiversity afloat

Island conservation in the longer term Conservation of biodiversity on islands is important globally because islands are home to more than 20% of the terrestrial plant and vertebrate species in the world, within less than 5% of the global terrestrial area. Endemism on islands is a magnitude higher than on continents [1]; ten of the 35 biodiversity hotspots in the world are entirely, or largely consist of, islands [2]. Yet this diversity is threatened: over half of all recent extinctions have occurred on islands, which currently harbor over one-third of all terrestrial species facing imminent extinction [3] (Figure 1). In response to the biodiversity crisis, island conservation has been an active field of research and action. Hundreds of invasive species eradications and endangered species translocations have been successfully completed [4–6]. However, despite climate change being an increasing research focus generally, its impacts on island biodiversity are only just beginning to be investigated. For example, invasive species eradications on islands have been prioritized largely by threats to native biodiversity, eradication feasibility, economic cost, and reinvasion potential, but have never considered the threat of sea-level rise. Yet, the probability and extent of island submersion would provide a relevant metric for the longevity of long-term benefits of such eradications.