bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the QuantiFERON-TB and tuberculin skin test for detection of latent tuberculosis infection in cancer patients in a developing country
Authors: Galindo Javier Leonardo , Galeano Adriana Catalina , Suarez-Zamora David Alfonso , Callejas Ana Milena , Caicedo-Verástegui Mónica Patricia , Londoño Darío , García-Herreros Luis Gerardo , Ospina-Serrano Aylen Vanessa , Saavedra Alfredo , Garcíaherreros Plutarco , Palacios Diana María , Baldión Margarita 
Published: October 2019

Cancer patients have an increased risk of reactivation of latent tuberculosis infection. It is unknown which strategy on screening should be used in this population in developing countries. We aimed to determine the concordance between the tuberculin skin test (TST) and QuantiFERON®-TB (QFT) assay in order to diagnose latent tuberculosis infection in cancer patients.We conducted a cross-sectional study of the agreement of diagnostic tests. Prevalence and agreement between tests were calculated. A logistic regression to assess predictors of discordance was performed. The accuracy of the TST to predict QFT results by a receiver operating characteristic (ROC) curve was evaluated.We included 149 adults with cancer without active tuberculosis. Prevalence of latent tuberculosis infection was 21.5% (n=32), defined as positive results on either test. Test agreement was moderate for the diagnosis of latent tuberculosis infection (κ=0.43, 90% CI 0.26–0.6). No predictor was associated with the chance of discordant results. Agreement improved slightly using a cut-off point ≥8 mm (κ=0.5, 90% CI 0.35–0.66).In a moderate-incidence setting, a moderate agreement was found between tests in cancer patients. Modification of the cut-off points of test results achieved marginally better agreement between the TST and QFT.
VarSight: prioritizing clinically reported variants with binary classification algorithms
Authors:   Undiagnosed Diseases Network, Holt James M. , Wilk Brandon , Birch Camille L. , Brown Donna M. , Gajapathy Manavalan , Moss Alexander C. , Sosonkina Nadiya , Wilk Melissa A. , Anderson Julie A. , Harris Jeremy M. , Kelly Jacob M. , Shaterferdosian Fariba , Uno-Antonison Angelina E. , Weborg Arthur , Worthey Elizabeth A. 
Published: October 2019

Abstract

Background
When applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient’s phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance.

Methods
We tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network.

Results
We treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20.

Conclusions
We demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets.
A modular steroid-inducible gene expression system for use in rice
Authors: Vlad Daniela , Abu-Jamous Basel , Wang Peng , Langdale Jane A. 
Published: October 2019

AbstractBackgroundChemically inducible systems that provide both spatial and temporal control of gene expression are essential tools, with many applications in plant biology, yet they have not been extensively tested in monocotyledonous species.ResultsUsing Golden Gate modular cloning, we have created a monocot-optimized dexamethasone (DEX)-induciblepOp6/LhGR system and tested its efficacy in rice using the reporter enzyme β-glucuronidase (GUS). The system is tightly regulated and highly sensitive to DEX application, with 6 h of induction sufficient to induce high levels of GUS activity in transgenic callus. In seedlings, GUS activity was detectable in the root after in vitro application of just 0.01 μM DEX. However, transgenic plants manifested severe developmental perturbations when grown on higher concentrations of DEX. The direct cause of these growth defects is not known, but the rice genome contains sequences with high similarity to the LhGR target sequencelacO,suggesting non-specific activation of endogenous genes by DEX induction. These off-target effects can be minimized by quenching with isopropyl β-D-1-thiogalactopyranoside (IPTG).ConclusionsOur results demonstrate that the system is suitable for general use in rice, when the method of DEX application and relevant controls are tailored appropriately for each specific application.
Construction of genetic linkage map and identification of a novel major locus for resistance to pine wood nematode in Japanese black pine (Pinus thunbergii)
Authors: Hirao Tomonori , Matsunaga Koji , Hirakawa Hideki , Shirasawa Kenta , Isoda Keiya , Mishima Kentaro , Tamura Miho , Watanabe Atsushi 
Published: October 2019

AbstractBackgroundPine wilt disease (PWD), which is caused by the pine wood nematode (PWN)Bursaphelenchus xylophilus, is currently the greatest threat to pine forests in Europe and East Asian countries including Japan. Constructing a detailed linkage map of DNA markers and identifying PWD resistance genes/loci lead to improved resistance inPinus thunbergii, as well as otherPinusspecies that are also susceptible to PWD.ResultsA total F1mapping population of 188 individuals derived from a cross between the PWD-resistantP. thunbergiivarieties ‘Tanabe 54’ (resistant rank 2 to PWD) and ‘Tosashimizu 63’ (resistant rank 4 to PWD) was inoculated with PWN, and was evaluated for disease symptoms. To perform linkage analysis for PWN resistance, a set of three maps was constructed; two parental maps generated using the integrated two-way pseudo-testcross method, and a consensus map with population-type cross-pollination. The linkage map of ‘Tanabe 54’ consisted of 167 loci, and covered 14 linkage groups (LGs), with a total genetic distance of 1214.6 cM. The linkage map of ‘Tosashimizu 63’ consisted of 252 loci, and covered 14 LGs, with a total genetic distance of 1422.1 cM. The integrated consensus map comprised 12 LGs with the basic chromosome number ofP. thunbergii, and a total genetic distance of 1403.6 cM. Results from quantitative trait loci (QTL) analysis using phenotype data and linkage maps indicated that PWN resistance is controlled by a single dominant allele, which was derived from the ‘Tanabe 54’ female parent. This major QTL was located on linkage group 3 and was designatedPWD1forPINE WILT DISEASE 1.ConclusionsThePWD1locus is a major resistance QTL located on thePinusconsensus LG03 that acts in a dominant manner to confer pine wood nematode resistance. Information from the present study will be useful forP. thunbergiibreeding programs to improve resistance to PWD, and also to help identify susceptibility genes inPinusspecies.
Serum uric acid and risk of cardiovascular mortality: a systematic review and dose-response meta-analysis of cohort studies of over a million participants
Authors: Rahimi-Sakak Fatemeh , Maroofi Mahsa , Rahmani Jamal , Bellissimo Nick , Hekmatdoost Azita 
Published: October 2019

Abstract

Background
Cardiovascular disease (CVD) is the leading cause of death worldwide. Some studies have suggested anassociation between serum uric acid levels and cardiovascular mortality; however, the results have not been summarized in a meta-analysis.

Methods
A comprehensive search of all related studies until April 2018was performed in MEDLINE/PubMed and Scopus databases DerSimonianand Laird random-effects models were used to combine hazard ratios (HRs) with 95% confidence intervals (CIs). Dose-response analysis was also carried out.

Results
Thirty-two studies containing forty-four arms with 1,134,073 participants reported association between uric acid and risk of CVD mortality were included in our analysis. Pooled results showed a significant positive association between uric acid levels and risk of CVD mortality (HR 1.45, 95% CI 1.33–1.58, I2 = 79%). Sub-group analysis showed this relationshipwasstronger in women compared to men. Moreover, there was a significant non-linear association between uric acid levels and the risk of CVD mortality (r = 0.0709, p = 0.001).

Conclusion
Our analysis indicates a positive dose-response association between SUA and CVD mortality risk.
The first case of Acrophialophora levis-induced severe pneumonia: a case report and literature review
Authors: Huang Junyun , Liu Zhiping 
Published: October 2019

Abstract

Background
In recent years, some rare fungi have been increasingly recognized as new human pathogens. Here we reported the first fatal case of human severe pneumonia complicated by multiple organ dysfunction caused by Acrophialophora levis infection. However, its pathogenic mechanism and risk factors are unknown. Acrophialophora genus has only reported in six cases of human infection worldwide, but it has not been reported previously in China.

Case presentation
A 71-year-old male patient with severe pneumonia complicated with multiple organ dysfunction caused by A. levis infection. The fungal identification was based on micromorphology and sequence analysis of the internal transcriptional spacer (ITS) of ribosomal RNA genes recovered from lower respiratory tract secretions. The microbial characteristics, sensitivity to antifungal drugs of this isolated A. levis were studied. Anti-infective regimen, liposomal amphotericin B combined with tegacycline, was used to prevent infection. The next day, the fever decreased, body temperature fluctuated between 36.5 and 37.8 degree, cough and sputum decreased, and sputum volume decreased, with oxygen uptake for 5 L/min, blood oxygen saturation over 95%. After 17 days of treatment, CT reexamination showed that the lesions in the right lung and left upper lung were absorbed and pleural effusion was reduced. The next 8 days, the patient asked to return to the local hospital for treatment. The local hospital stopped using liposomal amphotericin B because of the absence of liposomal amphotericin B, and died of respiratory failure 2 days later.

Conclusions
This study is the first to report the occurrence, risk factors, molecular determinants, microbial characteristics and susceptibility to antifungal agents of A. levis infection in China. In addition, six published cases of human infection with Acrophialophora were reviewed.
Increased activation of the pregenual anterior cingulate cortex to citalopram challenge in migraine: an fMRI study
Authors: Edes Andrea Edit , McKie Shane , Szabo Edina , Kokonyei Gyongyi , Pap Dorottya , Zsombok Terezia , Magyar Mate , Csepany Eva , Hullam Gabor , Szabo Adam Gyorgy , Kozak Lajos Rudolf , Bagdy Gyorgy , Juhasz Gabriella 
Published: October 2019

Abstract

Background
The anterior cingulate cortex (ACC) is a key structure of the pain processing network. Several structural and functional alterations of this brain area have been found in migraine. In addition, altered serotonergic neurotransmission has been repeatedly implicated in the pathophysiology of migraine, although the exact mechanism is not known. Thus, our aim was to investigate the relationship between acute increase of brain serotonin (5-HT) level and the activation changes of the ACC using pharmacological challenge MRI (phMRI) in migraine patients and healthy controls.

Methods
Twenty-seven pain-free healthy controls and six migraine without aura patients participated in the study. All participant attended to two phMRI sessions during which intravenous citalopram, a selective serotonin reuptake inhibitor (SSRI), or placebo (normal saline) was administered. We used region of interest analysis of ACC to compere the citalopram evoked activation changes of this area between patients and healthy participants.

Results
Significant difference in ACC activation was found between control and patient groups in the right pregenual ACC (pgACC) during and after citalopram infusion compared to placebo. The extracted time-series showed that pgACC activation increased in migraine patients compared to controls, especially in the first 8–10 min of citalopram infusion.

Conclusions
Our results demonstrate that a small increase in 5-HT levels can lead to increased phMRI signal in the pregenual part of the ACC that is involved in processing emotional aspects of pain. This increased sensitivity of the pgACC to increased 5-HT in migraine may contribute to recurring headache attacks and increased stress-sensitivity in migraine.
Determinants of prenatal care use and HIV testing during pregnancy: a population-based, cross-sectional study of 7080 women of reproductive age in Mozambique
Authors: Yaya Sanni , Oladimeji Olanrewaju , Oladimeji Kelechi Elizabeth , Bishwajit Ghose 
Published: October 2019

Abstract

Background
In low-income countries with poor coverage of healthcare services such as Mozambique, antenatal care serves as a vital tool for providing life-saving and cost-effective services for pregnant mothers. Nonetheless, many countries in Africa, including Mozambique, are struggling to attain an optimum level of antenatal care (at least 4 visits) utilisation among pregnant women. In the present study, we aimed to assess the sociodemographic and economic factors associated with antenatal care use in Mozambique.

Methods
Cross-sectional data from the latest round of Mozambique Demographic and Health Survey (2011) on women aged 15–49 years (n = 7080) were analysed. The outcome measures were early and adequate antenatal visit and HIV tests during the last pregnancy. Data were analysed using descriptive and multivariate regression methods. The predictor variables included various demographic (e.g. age, parity), empowerment (e.g. type of employment, household wealth status) and sociocultural factors (e.g. ethnicity, religion).

Results
Of the 7080 women whose data was analyzed, 15.3 and 60.1% had early and adequate ANC visits respectively while 75.4% received HIV test during ANC visits. The odds of early ANC visits were higher [OR = 1.300, 95%CI = 1.062,1.592] among women in the rural areas compared with those in the urban areas. However, participants in rural areas had lower odds [OR = 0.788, 0.687,0.902] of receiving HIV tests during ANC visits. Women in the urban areas with secondary [OR = 1.296, 95%CI = 1.007,1.666] and higher [OR = 1.663, 95%CI = 1.052,2.628] education had higher odds of having early ANC visit. Those in the higher wealth quintiles also had significantly increased odds of using all three types of ANC indicators, particularly for rural women in the highest wealth quintile [OR = 4.776, 95%CI = 1.250,18.24]. Being within the higher wealth quintiles was found to significantly increase the odds of using all three types of ANC indicators, particularly women from rural areas with highest wealth quintile [OR = 4.776, 95%CI = 1.250,18.24].

Conclusion
About two-fifth of the women in Mozambique are not using adequate antenatal care and about and a quarter do not take HIV tests during pregnancy. The sources of low and unequal use of these vital health services might be rooted in women’s socioeconomic status and cultural issues that require special policy and research attention.
Overexpression of iASPP is required for autophagy in response to oxidative stress in choriocarcinoma
Authors: Chan Ka-Kui , Wong Esther Shuk-Ying , Wong Ivy Tsz-Lo , Cheung Claire Ling-Yang , Wong Oscar Gee-Wan , Ngan Hextan Yuen-Sheung , Cheung Annie Nga-Yin 
Published: October 2019

Abstract

Background
Gestational trophoblastic disease (GTD) is a heterogeneous group of diseases developed from trophoblasts. ASPP (Ankyrin-repeat, SH3-domain and proline-rich region containing protein) family proteins, ASPP1 and ASPP2, have been reported to be dysregulated in GTD. They modulate p53 activities and are responsible for multiple cellular processes. Nevertheless, the functional role of the ASPP family inhibitory member, iASPP, is not well characterized in GTD.

Methods
To study the functional role of iASPP in GTD, trophoblastic tissues from normal placentas, hydatidiform mole (HM) and choriocarcinoma were used for immunohistochemistry, whereas siRNAs were used to manipulate iASPP expression in choriocarcinoma cell lines and study the subsequent molecular changes.

Results
We demonstrated that iASPP was overexpressed in both HM and choriocarcinoma when compared to normal placenta. Progressive increase in iASPP expression from HM to choriocarcinoma suggests that iASPP may be related to the development of trophoblastic malignancy. High iASPP expression in HM was also significantly associated with a high expression of autophagy-related protein LC3. Interestingly, iASPP silencing retarded the growth of choriocarcinoma through senescence instead of induction of apoptosis. LC3 expression decreased once iASPP was knocked down, suggesting a downregulation on autophagy. This may be due to iASPP downregulation rendered decrease in Atg5 expression and concomitantly hindered autophagy in choriocarcinoma cells. Autophagy inhibition per se had no effect on the growth of choriocarcinoma cells but increased the susceptibility of choriocarcinoma cells to oxidative stress, implying a protective role of iASPP against oxidative stress through autophagy in choriocarcinoma.

Conclusions
iASPP regulates growth and the cellular responses towards oxidative stress in choriocarcinoma cells. Its overexpression is advantageous to the pathogenesis of GTD. (266 words).
Myopic Laser-Assisted Subepithelial Keratectomy (LASEK) outcomes using three different excimer laser platforms: a retrospective observational study
Authors: Rodríguez-Pérez Isabel , Gros-Otero Juan , Teus Miguel A. , Cañones Rafael , García-González Montserrat 
Published: October 2019

Abstract

Background
To compare the visual and refractive outcomes after myopic LASEK using three different excimer lasers and standardized surgical and mitomycin C (MMC) application protocols.

Methods
In this retrospective, observational cohort study, we examined 122 eyes treated with Allegretto, 135 eyes treated with Esiris and 137 eyes treated with Technolas excimer lasers. All eyes were treated under the same surgical protocol, and a standardized MMC dosage was used. The three groups were refraction-matched, and both visual and refractive outcomes were evaluated at 1 and 7 days and 1 and 3 months after surgery.

Results
At 3 months postsurgery, Allegretto provided significantly better outcomes than Esiris and Technolas in terms of postoperative uncorrected distance visual acuity (UDVA) (1.11 ± 0.2 vs 1.01 ± 0.2 vs 0.98 ± 0.2) (P = 0.0001), corrected distance visual acuity (CDVA) (1.13 ± 0.2 vs 1.10 ± 0.1 vs 1.04 ± 0.2) (P = 0.0001), residual sphere (− 0.01 ± 0.2 vs + 0.29 ± 0.7 vs + 0.27 ± 0.6) (P = 0.0001), and efficacy index (0.99 ± 0.2 vs 0.90 ± 0.2 vs 0.91 ± 0.2) (P = 0.0004).

Conclusions
We found slightly better visual and refractive outcomes in the Allegretto group at 3 months post-op after LASEK with MMC to correct myopia.
Necrotizing enterocolitis after intravitreal bevacizumab in an infant with Incontinentia Pigmenti – a case report
Authors: Kunzmann S. , Ngyuen T. , Stahl A. , Walz J. M. , Nentwich M. M. , Speer C. P. , Ruf K. 
Published: October 2019

AbstractBackgroundIncontinentia Pigmenti is a rare disease affecting multiple organs. Fifty of patients show affection of the eye with retinopathy and possible amaurosis being the worst outcome. Treatment has commonly been panretinal laser coagulation but intravitreal application of bevacizumab as VEGF-inhibitor has shown to effectively suppress retinal neovascularization.Case presentationA six-week-old female infant with Incontinentia Pigmenti developed a foudroyant necrotizing enterocolitis shortly after intravitreal injection of bevazicumab due to a retinopathy with impending tractional detachment of the left eye. Since the onset of abdominal symptoms occurred immediately after the intravitreal application, a link between the two events seemed likely. Sequential analyses of the VEGF serum concentrations showed a massive suppression of endogenous VEGF with only a very slow recovery over weeks. Such a severe systemic adverse event has not been reported after intravitreal treatment with bevacizumab in an infant.ConclusionThis case report shows a relevant systemic uptake of bevacizumab after intravitreal application as suppressed VEGF levels show. There seems to be a connection between suppressed VEGF levels and the onset of necrotizing enterocolitis. Therefore, treatment with bevacizumab should be carefully considered and further research is needed to assess this drug’s safety profile.
Development of the Adjusted Wind Chill Equivalent Temperature (AWCET) for cold mortality assessment across a subtropical city: validation and comparison with a spatially-controlled time-stratified approach
Authors: Ho Hung Chak , Wong Man Sing , Abbas Sawaid , Zhu Rui 
Published: October 2019

Abstract

Background
Global warming has reduced the adaptability of the people living in subtropical regions to cope up with cold stress due to lengthening of hot days and shortening of transition period from hot to cold weather. However, existing studies on measuring cold stress are based on biometeorological indices designed for temperate regions. This may overestimate the impact of wind chill on mortality risk in subtropical cities.

Methods
This study developed an Adjusted Wind Chill Equivalent Temperature (AWCET) index. A spatially-controlled time-stratified approach was applied to evaluate the ability of AWCET for estimating cold mortality in subtropical cities, based on a mortality dataset (2008–2012) in Hong Kong.

Results
The use of AWCET could indicate increase in all-cause, cardiovascular, respiratory, and cancer-related mortality risk during the days with average temperature < = 1st [11.0 °C], <= 3rd [12.6 °C] and < = 5th [13.4 °C] percentiles. The results were stable and consistent based on both log-linear and curve-linear relationships between AWCET and mortality risk. AWCET was also compared with the New Wind Chill Equivalent Temperature (NWCET) designed for temperate regions, and has found that higher magnitude of mortality risk would be found when using AWCET for assessing all-cause and cause-specific mortality in Hong Kong, for days with average temperature < = 1st, <= 3rd and < = 5th percentiles.

Conclusions
AWCET is validated to be effective to access cold mortality in the context of subtropical cities. The use of AWCET may enhance the cold weather warning system in subtropical cities, as a supplementary tool to help demonstrating small administrative-level perceived temperature with volunteered geographic information.