bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pneumocystis pneumonia occurrence and prophylaxis duration in kidney transplant recipients according to perioperative treatment with rituximab
Authors: Kim Young Hoon , Kim Jee Yeon , Kim Dong Hyun , Ko Youngmin , Choi Ji Yoon , Shin Sung , Jung Joo Hee , Park Su-Kil , Kim Sung-Han , Kwon Hyunwook , Han Duck Jong 
Published: March 2020

Abstract
Background
Pneumocystis pneumonia (PCP) is a life-threatening fungal infection that can occur in kidney transplantation (KT) recipients. A growing number of KT recipients are receiving perioperative treatment with rituximab, which is associated with prolonged B-cell depletion and possible risk of PCP occurrence; however, the optimal prophylaxis duration according to rituximab treatment is yet unknown. We compared the occurrence of PCP and the duration of prophylaxis in KT recipients according to rituximab treatment.

Methods
We retrospectively analyzed 2110 patients who underwent KT between January 2009 and December 2016, who were divided into non-Rituximab group (n = 1588, 75.3%) and rituximab group (n = 522, 24.7%).

Results
In the rituximab group, the estimated number needed to treat (NNT) for prophylaxis prolongation from 6 to 12 months was 29.0 with a relative risk reduction of 90.0%. In the non-rituximab group, the estimated NNT value was 133.3 and the relative risk reduction was 66.4%. Rituximab treatment (hazard ratio (HR) = 3.09; P <  0.01) and acute rejection (HR = 2.19; P = 0.03) were significant risk factors for PCP in multivariate analysis.

Conclusions
Our results suggest that maintaining PCP prophylaxis for 12 months may be beneficial in KT recipients treated with rituximab for desensitization or acute rejection treatment.
Outcomes in acute kidney injury in noncritically ill patients lately referred to nephrologist in a developing country: a comparison of AKIN and KDIGO criteria
Authors: Nascimento Ginivaldo Victor Ribeiro do , Silva Marcela do Nascimento , Carvalho Neto Juarez Duarte de , Feitosa Filho Ludgero Ribeiro , Antão Jessica Duarte 
Published: March 2020

Abstract
Background
In low-middle-income countries (LMICs), data regarding acute kidney injury (AKI) are scarce. AKI patients experience delayed diagnosis. This study aimed to evaluate whether delayed nephrologist consultation (NC) affected outcomes of AKI patients and compare Acute Kidney Injury Network (AKIN) and Kidney Disease: Improving Global Outcomes (KDIGO).

Methods
An observational, retrospective study was conducted in a tertiary public hospital in an LMIC.

Results
Overall, 103 AKI patients were analysed. In-hospital mortality was 61.16%, and dialysis was required in 38.83%. NC took place after 48 h in 68.93% of the patients. Mean time for NC was 5.22 ± 4.30 days. At NC, serum creatinine was 4.48 (±3.40) mg/dL and blood urea nitrogen was 68.21 (± 35.02) mg/dL. The AKIN and KDIGO stage stratifications were identical; KDIGO stage 3 was seen in 58.25% of the patients. The group with NC >  4 days had a mortality rate of 74.46% and the group with NC ≤ 4 days had a mortality rate of 50% (p = 0.011). Multivariate analysis showed that haemodialysis was independently associated with mortality. NC >  4 days was associated with death [odds ratio 2.66 (95% confidence interval, 1.36–4.35), p = 0.001]. Logistic regression showed an OR of 1.20 (95% CI, 1.05–1.37) (p = 0.008) for each day of delayed NC.

Conclusion
Delayed NC was associated with mortality even after adjustments, as was haemodialysis, though marginally. In AKI patients with NC > 4 days, there was a high prevalence of KDIGO stage 3, and AKIN and KDIGO criteria were identical.
Validation of the Chinese version of the Amsterdam Preoperative Anxiety and Information Scale (APAIS)
Authors: Wu Hao , Zhao Xin , Chu Shuaishuai , Xu Fangxia , Song Jia , Ma Zhengliang , Gu Xiaoping 
Published: March 2020

AbstractBackgroundPreoperative anxiety is an unpleasant state of tension that may impact patients’ post-operative pain and satisfaction. The level of preoperative anxiety should be routinely identified. The Amsterdam Preoperative Anxiety and Information Scale (APAIS) is a self-reported questionnaire that is used to quickly assess preoperative anxiety and information needs with good psychometric properties.ObjectivesTo validate the Chinese version of the Amsterdam Preoperative Anxiety and Information Scale (APAIS) and to explore coping strategies used by patients in dealing with surgery and anesthetic.MethodsThe cross-cultural validation of APAIS involved the translation of a Chinese version of APAIS and an investigation of its psychometric properties and clinical applicability. Forward-back translation and a pilot study were performed to produce a Chinese adaptation of APAIS. The inpatients of the orthopedic, otolaryngology, and general surgery department scheduled for general anesthesia surgery were enrolled to complete psychometric testing. The reliability was assessed using Cronbach’s alpha. Exploratory factor analysis and confirmatory factor analysis were calculated to assess construct validity. The criteria validity was analyzed using the correlation between APAIS and State-trait anxiety inventory-state (STAI-S) and Visual analogue scale-anxiety (VAS-A). Coping styles were evaluated using the Medical Coping Modes Questionnaire (MCMQ) score that covered three domains: confrontation, avoidance, and resignation. The impact of different coping styles on patients’ anxiety was explored.ResultsA total of 204 valid questionnaires were collected the day before surgery. Cronbach’s alpha coefficients were 0.862 for the anxiety scale and 0.830 for the information scale. Exploratory factor analysis with oblique rotation revealed two factors that explained 76.45% of the total variances. A confirmatory factor analysis showed a two-factor model with an adequate model fit (root mean square error of approximation: 0.073, goodness-of-fit: 0.966). The APAIS anxiety score significantly correlated with STAI-S (r = 0.717,P < 0.01) and VAS-A (r = 0.720,P < 0.01). For the three coping strategies, preoperative anxiety had a low correlation with confrontation (r = 0.33,P < 0.01) and resignation (r = 0.22,P < 0.05).ConclusionsThe Chinese version of APAIS is a valid and reliable instrument for assessing preoperative anxiety. Use of this measurement tool for Chinese patients is feasible and shows promising results.
Response to: Simpson’s Paradox is suppression, but Lord’s Paradox is neither: clarification of and correction to Tu, Gunnell, and Gilthorpe (2008) by Nickerson CA & Brown NJL (https://doi.org/10.1186/1742-7622-5-2)
Authors: Gilthorpe Mark S. , Tu Yu-Kang 
Published: March 2020

AbstractWe commend Nickerson and Brown on their insightful exposition of the mathematical algebra behind Simpson’s paradox, suppression and Lord’s paradox; we also acknowledge there can be differences in how Lord’s paradox is approached analytically, compared to Simpson’s paradox and suppression, though not in every example of Lord’s paradox. Furthermore, Simpson’s paradox, suppression and Lord’s paradox ask the same contextual questions, seeking to understand if statistical adjustment is valid and meaningful, identifying which analytical option is correct. In our exposition of this, we focus on the perspective of context, which must invoke causal thinking. From a causal thinking perspective, Simpson’s paradox, suppression and Lord’s paradox present very similar analytical challenges.
Systematic analysis of ovarian cancer platinum-resistance mechanisms via text mining
Authors: Li Haixia , Li Jinghua , Gao Wanli , Zhen Cheng , Feng Limin 
Published: March 2020

Abstract
Background
Platinum resistance is an important cause of clinical recurrence and death for ovarian cancer. This study tries to systematically explore the molecular mechanisms for platinum resistance in ovarian cancer and identify regulatory genes and pathways via text mining and other methods.

Methods
Genes in abstracts of associated literatures were identified. Gene ontology and protein-protein interaction (PPI) network analysis were performed. Then co-occurrence between genes and ovarian cancer subtypes were carried out followed by cluster analysis.

Results
Genes with highest frequencies are mostly involved in DNA repair, apoptosis, metal transport and drug detoxification, which are closely related to platinum resistance. Gene ontology analysis confirms this result. Some proteins such as TP53, HSP90, ESR1, AKT1, BRCA1, EGFR and CTNNB1 work as hub nodes in PPI network. According to cluster analysis, specific genes were highlighted in each subtype of ovarian cancer, indicating that various subtypes may have different resistance mechanisms respectively.

Conclusions
Platinum resistance in ovarian cancer involves complicated signaling pathways and different subtypes may have specific mechanisms. Text mining, combined with other bio-information methods, is an effective way for systematic analysis.
Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium
Authors: Kazakevych Juri , Denizot Jérémy , Liebert Anke , Portovedo Mariana , Mosavie Mia , Jain Payal , Stellato Claudia , Fraser Claire , Corrêa Renan Oliveira , Célestine Marina , Mattiuz Raphaël , Okkenhaug Hanneke , Miller J. Ross , Vinolo Marco Aurélio Ramirez , Veldhoen Marc , Varga-Weisz Patrick 
Published: March 2020

Abstract
Background
How intestinal epithelial cells interact with the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is a conserved chromatin remodeling factor with a poorly understood tissue function. As this factor is highly expressed in the stem and proliferative zones of the intestinal epithelium, we explore its role in this tissue.

Results
Specific deletion of Smarcad1 in the mouse intestinal epithelium leads to colitis resistance and substantial changes in gene expression, including a striking increase of expression of several genes linked to innate immunity. Absence of Smarcad1 leads to changes in chromatin accessibility and significant changes in histone H3K9me3 over many sites, including genes that are differentially regulated upon Smarcad1 deletion. We identify candidate members of the gut microbiome that elicit a Smarcad1-dependent colitis response, including members of the poorly understood TM7 phylum.

Conclusions
Our study sheds light onto the role of the chromatin remodeling machinery in intestinal epithelial cells in the colitis response and shows how a highly conserved chromatin remodeling factor has a distinct role in anti-microbial defense. This work highlights the importance of the intestinal epithelium in the colitis response and the potential of microbial species as pharmacological and probiotic targets in the context of inflammatory diseases.
GtxA is a virulence factor that promotes a Th2-like response during Gallibacterium anatis infection in laying hens
Authors: Tang Bo , Pors Susanne E. , Kristensen Bodil M. , Skjerning Ragnhild Bager J. , Olsen Rikke H. , Bojesen Anders M. 
Published: March 2020

AbstractGtxA, a leukotoxic RTX-toxin, has been proposed a main virulence factor of Gallibacterium anatis. To evaluate the impact of GtxA during infection, we experimentally infected laying hens with a G. anatis wild-type (WT) strain and its isogenic gtxA deletion mutant (ΔgtxA), respectively, and monitored the birds during a 6 day period. Birds inoculated with ΔgtxA had significantly reduced gross lesions and microscopic changes compared to the birds inoculated with the WT strain. To assess the host response further, we quantified the expression of pro-inflammatory cytokines and apoptosis genes by RT-qPCR. In the ovarian tissue, the expression levels of IL-4 and TNF-α were significantly lower in the ΔgtxA group compared to the WT group, while IL-6 and IL-10 levels appeared similar in the two groups. In the spleen tissue of ΔgtxA infected chickens, IL-4 expression was also lower compared to the WT infected chickens. The results indicated that GtxA plays a key role in an acute cytokine-mediated Th2-like response against G. anatis infection in the ovary tissue. The pro-inflammatory response in the ovary tissue of birds inoculated with ΔgtxA mutant was thus significantly lower than the wild-type response. This was, at least partly, supported by the apoptosis gene expression levels, which were significantly higher in the ΔgtxA mutant compared to the wild-type infected chickens. In conclusion, GtxA clearly plays an important role in the pathogenesis of G. anatis infections in laying hens. Further investigations into the specific factors regulating the host response is however needed to provide a more complete understanding of the bacteria-host interaction.
The role of poly(ADP-ribose) polymerase inhibitors in the treatment of cancer and methods to overcome resistance: a review
Authors: Patel Mausam , Nowsheen Somaira , Maraboyina Sanjay , Xia Fen 
Published: March 2020

AbstractPoly(ADP-ribose) polymerase (PARP) inhibitors represent one of the successful novel approaches to targeted cancer treatment. Indeed, the US Food and Drug Administration (FDA) has recently approved PARP inhibitors for the treatment of breast and ovarian cancers. Despite the proven efficacy of these agents, certain challenges remain with their use. Among the most important are primary and secondary resistance. Here, we review the mechanism of action of PARP inhibitors and their ability to exploit certain inherent deficiencies among malignant cells to improve cell killing, with a focus on deficiencies in homologous recombination among cells with BRCA1 and BRCA2 mutations. Moreover, we discuss the different mechanisms of resistance including development of secondary resistance and strategies to overcome them. Finally, we discuss the limitations of novel therapeutic interventions and possible future studies to exploit biochemical pathways in order to improve therapeutic efficacy of PARP inhibitors.
RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs
Authors: Li Leyuan , Ning Zhibin , Zhang Xu , Mayne Janice , Cheng Kai , Stintzi Alain , Figeys Daniel 
Published: March 2020

AbstractBackgroundHuman-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota. However, our understanding of such effects is limited due to a lack of rapid and scalable assay to comprehensively assess microbiome responses to drugs. Drugs and other compounds can drastically change the overall abundance, taxonomic composition, and functions of a gut microbiome.ResultsHere, we developed an approach to screen compounds against individual microbiomes in vitro, using metaproteomics to both measure absolute bacterial abundances and to functionally profile the microbiome. Our approach was evaluated by testing 43 compounds (including 4 antibiotics) against 5 individual microbiomes. The method generated technically highly reproducible readouts, including changes of overall microbiome abundance, microbiome composition, and functional pathways. Results show that besides the antibiotics, the compounds berberine and ibuprofen inhibited the accumulation of biomass during in vitro growth of the microbiota. By comparing genus and species level-biomass contributions, selective antibacterial-like activities were found with 35 of the 39 non-antibiotic compounds. Seven of the compounds led to a global alteration of the metaproteome, with apparent compound-specific patterns of functional responses. The taxonomic distributions of altered proteins varied among drugs, i.e., different drugs affect functions of different members of the microbiome. We also showed that bacterial function can shift in response to drugs without a change in the abundance of the bacteria.ConclusionsCurrent drug-microbiome interaction studies largely focus on relative microbiome composition and microbial drug metabolism. In contrast, our workflow enables multiple insights into microbiome absolute abundance and functional responses to drugs. The workflow is robust, reproducible, and quantitative and is scalable for personalized high-throughput drug screening applications.
How to tell the difference between a model and a digital twin
Authors: Wright Louise , Davidson Stuart 
Published: March 2020

Abstract“When I use a word, it means whatever I want it to mean”: Humpty Dumpty in Alice’s Adventures Through The Looking Glass, Lewis Carroll. “Digital twin” is currently a term applied in a wide variety of ways. Some differences are variations from sector to sector, but definitions within a sector can also vary significantly. Within engineering, claims are made regarding the benefits of using digital twinning for design, optimisation, process control, virtual testing, predictive maintenance, and lifetime estimation. In many of its usages, the distinction between a model and a digital twin is not made clear. The danger of this variety and vagueness is that a poor or inconsistent definition and explanation of a digital twin may lead people to reject it as just hype, so that once the hype and the inevitable backlash are over the final level of interest and use (the “plateau of productivity”) may fall well below the maximum potential of the technology. The basic components of a digital twin (essentially a model and some data) are generally comparatively mature and well-understood. Many of the aspects of using data in models are similarly well-understood, from long experience in model validation and verification and from development of boundary, initial and loading conditions from measured values. However, many interesting open questions exist, some connected with the volume and speed of data, some connected with reliability and uncertainty, and some to do with dynamic model updating. In this paper we highlight the essential differences between a model and a digital twin, outline some of the key benefits of using digital twins, and suggest directions for further research to fully exploit the potential of the approach.
Geolocator study reveals east African migration route of Central European Common Terns
Authors: Kralj Jelena , Martinović Miloš , Jurinović Luka , Szinai Péter , Sütő Szandra , Preiszner Bálint 
Published: March 2020

Abstract
Background
The majority of European Common Terns (Sterna hirundo) migrate south along the western coast of Europe and Africa, while birds from eastern regions are known to cross the Mediterranean Sea from east to west or migrate along the eastern African coast. The migration route of north European terns wintering along the coast of western Africa was already described using geolocator data, while knowledge about movements of the European inland populations is based only on relatively scarce recoveries of ringed birds.

Methods
We used light-level geolocators in inland Common Tern colonies in Hungary and Croatia to study their migration route and to identify wintering areas along with stopover sites. Results revealed by geolocators were compared with recoveries of ringed birds.

Results
All tracked birds used the east African migration route with autumn stopovers at Lower Nile and in the southern part of the Red Sea, and short spring stopover in Israel. Terns wintered along Kenyan coasts and in the southern Mozambique Channel. Autumn migration lasted four times longer than spring migration.

Conclusions
This is the first geolocator study that describes the east African migration route of the Common Tern. Important stopover sites were identified. More studies of inland populations are needed to better elucidate tern winter movements.
Accuracy of static computer-assisted implant placement in anterior and posterior sites by clinicians new to implant dentistry: in vitro comparison of fully guided, pilot-guided, and freehand protocols
Authors: Abduo Jaafar , Lau Douglas 
Published: March 2020

Abstract
Background
One of the challenges encountered by clinicians new to implant dentistry is the determination and controlling of implant location. This study compared the accuracy of fully guided (FG) and pilot-guided (PG) static computer-assisted implant placement (sCAIP) protocols against the conventional freehand (FH) protocol for placing single anterior and posterior implants by recently introduced clinicians to implant dentistry.

Material and methods
Ten clinicians new to implant dentistry inserted one anterior (central incisor) and one posterior (first molar) implants per protocol in training maxillary models. The FG protocol involved drilling and implant placement through the guide, while the PG protocol controlled the pilot drilling only. The FH implant placement was completed without the aid of any guide. A total of 30 models were used, and 60 implants were inserted. The implant vertical, horizontal neck, horizontal apex, and angle deviations from planned positions were calculated.

Results
The FG protocol provided the most accurate implant placement in relation to horizontal neck (0.47 mm–0.52 mm), horizontal apex (0.71 mm–0.74 mm), and angle deviations (2.42o–2.61o). The vertical deviation was not significantly different among the different protocols. The PG protocol was generally similar to the FH protocol with a horizontal neck deviation of 1.01 mm–1.14 mm, horizontal apex deviation of 1.02 mm–1.35 mm, and angle deviation of 4.65o–7.79o. The FG protocol showed similarity in the accuracy of the anterior and posterior implants. There was a tendency for inferior accuracy for posterior implants compared with anterior implants for the PG and FH protocols.

Conclusions
In the hands of recently introduced clinicians to implant dentistry, it appears that the accuracy of the FG protocol was superior to the other protocols and was not influenced by the position of the implants. The PG and FH protocols showed inferior accuracy for posterior implants compared with anterior implants.
Effect of different shielding conditions on the stability of Cisplatin
Authors: Abe Tomoya , Matsumoto Daigo , Nakayama Toshiaki , Shimazaki Yukinari , Sagara Atsunobu , Kanehira Dan , Azechi Takuya , Sato Fumiaki , Sakai Hiroyasu , Yumoto Tetsuro , Kamei Junzo 
Published: March 2020

Abstract
Background
Because cisplatin (CDDP) decreases upon light exposure, it is necessary to prevent such exposure during administration. However, the shielding conditions employed are not uniform. Therefore, in this study, we examined the shielding effects of four shading covers, which are commonly used to ensure the stability of CDDP in clinical settings.

Methods
Four shielding conditions, along with a control, were tested under a 1000-Lux white fluorescent lamp at room temperature: aluminum foil (Al), brown shading cover (BSC), yellow shading cover (YSC), milky-white anti-exposure cover (MAC), and no shading cover (NSC). Under each shielding condition, the relationship between the wavelength and transmittance was monitored in the range of 200–800 nm. CDDP was diluted to three concentration levels: 50, 100, and 250 μg/mL. Furthermore, the amount of remaining CDDP and the pH in the solutions were measured for 120 h.

Results
We found that BSC, YSC, and MAC conditions allowed various levels of transmittance; however, Al could not completely transmit light at all wavelengths. Moreover, we showed that the CDDP decreased under MAC and NSC conditions in a time-dependent manner, whereas this decrease was prevented under Al, BSC, and YSC conditions till 120 h. We also demonstrated increases in pH under MAC and NSC conditions in a time-dependent manner, which was prevented under Al, BSC, and YSC conditions till 120 h. Similar results were observed for all three CDDP concentration levels. The results also indicated the approximate relationship between the amount of remaining CDDP and the pH increase.

Conclusions
Considering the opacity of each cover, our results suggest that BSC and YSC are useful and effective for minimizing CDDP degradation in clinical settings. Our results also indicate the alternatives for preparing, storing, and administering CDDP in clinical facilities, making the treatment schedule more flexible. Cumulatively, these findings indicate that the use of the appropriate shading covers, such as BSC or YSC, prevents the decrease in CDDP under fluorescent lighting, potentially contributing to achieving its full therapeutic effect.