bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation in practice for preoperative antibiotic prophylaxis: a survey from an academic tertiary referral center in the United States
Authors: Ailaney Nikhil , Zielinski Elizabeth , Doll Michelle , Bearman Gonzalo M. , Kates Stephen L. , Golladay Gregory J. 
Published: October 2021

Abstract
Background
Antibiotic surgical prophylaxis is a core strategy for prevention of surgical site infections (SSI). Despite best practice guidelines and known efficacy of antibiotic prophylaxis in decreasing SSI risk, there is often wide variation in its use. This study was designed to determine the individual perspectives of perioperative providers at an academic tertiary referral center regarding their knowledge of preoperative antibiotic choice, dosing, and timing.

Methods
A prospective survey was conducted amongst surgical and anesthesia team members involved in preoperative antibiotic decision making. The survey addressed ten key principles relating to preoperative antibiotic use, including antibiotic choice, timing and rate of infusion, and dosing. The survey was distributed among orthopaedic surgeons, residents, and anesthesia providers at their respective monthly service line meetings between August 2017 to June 2019. The data was stored and analyzed in a Microsoft Excel worksheet.

Results
A total of 73 providers completed the survey. Twenty-two (30 %) of the providers agreed and 47 (64 %) disagreed that both vancomycin and cefazolin are equally effective for antibiotic prophylaxis. As for antibiotic choice in patients with penicillin allergies, 37 (51 %) agreed with vancomycin, 21 (29 %) agreed with clindamycin, and 15 (21 %) disagreed with both alternatives. When providers were surveyed regarding the appropriateness of standard versus weight adjusted dosing, 67 (92 %) agreed that vancomycin should be weight adjusted and 63 (86 %) agreed that cefazolin should be weight adjusted.

Conclusions
There is no clear consensus amongst providers for which antibiotic to administer for antibiotic prophylaxis despite existing guidelines. Discrepancy also exists between orthopaedic surgery and anesthesia providers in regards to appropriate antibiotic choice for patients with reported penicillin allergies. Institutions should implement evidence-based protocols for preoperative antibiotic prophylaxis and continue to prospectively monitor compliance in order to identify any inconsistencies that could result in inappropriate antibiotic prophylaxis for patients.
Grass-like plants release general volatile cues attractive for gravid Anopheles gambiae sensu stricto mosquitoes
Authors: Bokore Getachew E. , Svenberg Linus , Tamre Richard , Onyango Patrick , Bukhari Tullu , Emmer Åsa , Fillinger Ulrike 
Published: October 2021

AbstractBackgroundUnderstanding the ecology and behaviour of disease vectors, including the olfactory cues used to orient and select hosts and egg-laying sites, are essential for the development of novel, insecticide-free control tools. Selected graminoid plants have been shown to release volatile chemicals attracting malaria vectors; however, whether the attraction is selective to individual plants or more general across genera and families is still unclear.MethodsTo contribute to the current evidence, we implemented bioassays in two-port airflow olfactometers and in large field cages with four live graminoid plant species commonly found associated with malaria vector breeding sites in western Kenya:Cyperus rotundusandC. exaltatusof the Cyperaceae family, andPanicum repensandCynodon dactylonof the Poaceae family. Additionally, we tested one Poaceae species,Cenchrus setaceus, not usually associated with water. The volatile compounds released in the headspace of the plants were identified using gas chromatography/mass spectrometry.ResultsAll five plants attracted gravid vectors, with the odds of a mosquito orienting towards the choice-chamber with the plant in an olfactometer being 2–5 times higher than when no plant was present. This attraction was maintained when tested with free-flying mosquitoes over a longer distance in large field cages, though at lower strength, with the odds of attracting a female 1.5–2.5 times higher when live plants were present than when only water was present in the trap.Cyperus rotundus,previously implicated in connection with an oviposition attractant, consistently elicited the strongest response from gravid vectors. Volatiles regularly detected were limonene, β-pinene, β-elemene and β-caryophyllene, among other common plant compounds previously described in association with odour-orientation of gravid and unfed malaria vectors.ConclusionsThe present study confirms that gravidAnopheles gambiaesensu stricto use chemical cues released from graminoid plants to orientate. These cues are released from a variety of graminoid plant species in both the Cyperaceae and Poaceae family. Given the general nature of these cues, it appears unlikely that they are exclusively used for the location of suitable oviposition sites. The utilization of these chemical cues for attract-and-kill trapping strategies must be explored under natural conditions to investigate their efficiency when in competition with complex interacting natural cues.Graphical abstract
On the role of dauer in the adaptation of nematodes to a parasitic lifestyle
Authors: Vlaar Lieke E. , Bertran Andre , Rahimi Mehran , Dong Lemeng , Kammenga Jan E. , Helder Johannes , Goverse Aska , Bouwmeester Harro J. 
Published: October 2021

AbstractNematodes are presumably the most abundant Metazoa on Earth, and can even be found in some of the most hostile environments of our planet. Various types of hypobiosis evolved to adapt their life cycles to such harsh environmental conditions. The five most distal major clades of the phylum Nematoda (Clades 8–12), formerly referred to as the Secernentea, contain many economically relevant parasitic nematodes. In this group, a special type of hypobiosis, dauer, has evolved. The dauer signalling pathway, which culminates in the biosynthesis of dafachronic acid (DA), is intensively studied in the free-living nematodeCaenorhabditis elegans, and it has been hypothesized that the dauer stage may have been a prerequisite for the evolution of a wide range of parasitic lifestyles among other nematode species. Biosynthesis of DA is not specific for hypobiosis, but if it results in exit of the hypobiotic state, it is one of the main criteria to define certain behaviour as dauer. Within Clades 9 and 10, the involvement of DA has been validated experimentally, and dauer is therefore generally accepted to occur in those clades. However, for other clades, such as Clade 12, this has hardly been explored. In this review, we provide clarity on the nomenclature associated with hypobiosis and dauer across different nematological subfields. We discuss evidence for dauer-like stages in Clades 8 to 12 and support this with a meta-analysis of available genomic data. Furthermore, we discuss indications for a simplified dauer signalling pathway in parasitic nematodes. Finally, we zoom in on the host cues that induce exit from the hypobiotic stage and introduce two hypotheses on how these signals might feed into the dauer signalling pathway for plant-parasitic nematodes. With this work, we contribute to the deeper understanding of the molecular mechanisms underlying hypobiosis in parasitic nematodes. Based on this, novel strategies for the control of parasitic nematodes can be developed.
Triatoma sordida (Hemiptera, Triatominae) from La Paz, Bolivia: an incipient species or an intraspecific chromosomal polymorphism?
Authors: Madeira Fernanda Fernandez , Delgado Luiza Maria Grzyb , Bittinelli Isadora de Freitas , de Oliveira Jader , Ravazi Amanda , dos Reis Yago Visinho , de Oliveira Ana Beatriz Bortolozo , Cristal Daniel Cesaretto , Galvão Cleber , de Azeredo-Oliveira Maria Tercília Vilela , da Rosa João Aristeu , Alevi Kaio Cesar Chaboli 
Published: October 2021

AbstractBackgroundTriatoma sordidais one of the main Chagas disease vectors in Brazil. In addition to Brazil, this species has already been reported in Bolivia, Argentina, Paraguay, and Uruguay. It is hypothesized that the insects currently identified asT. sordidaare a species subcomplex formed by three cytotypes (T. sordidasensu stricto [s.s.],T. sordidaLa Paz, andT. sordidaArgentina). With the recent description ofT. rosaifrom the Argentinean specimens, it became necessary to assess the taxonomic status ofT. sordidafrom La Paz, Bolivia, since it was suggested that it may represent a new species, which has taxonomic, evolutionary, and epidemiological implications. Based on the above, we carried out molecular and experimental crossover studies to assess the specific status ofT. sordidaLa Paz.MethodsTo evaluate the pre- and postzygotic barriers betweenT. sordidaLa Paz andT. sordidas.s., experimental crosses and intercrosses between F1 hybrids and between F2 hybrids were conducted. In addition, cytogenetic analyses of the F1 and F2 hybrids were applied with an emphasis on the degree of pairing between the homeologous chromosomes, and morphological analyses of the male gonads were performed to evaluate the presence of gonadal dysgenesis. Lastly, the genetic distance betweenT. sordidaLa Paz andT. sordidas.s. was calculated for theCYTB,ND1, andITS1genes.ResultsRegardless of the gene used,T. sordidaLa Paz showed low genetic distance compared toT. sordidas.s. (below 2%). Experimental crosses resulted in offspring for both directions, demonstrating that there are no prezygotic barriers installed between these allopatric populations. Furthermore, postzygotic barriers were not observed either (since the F1 × F1 and F2 × F2 intercrosses resulted in viable offspring). Morphological and cytogenetic analyses of the male gonads of the F1 and F2 offspring demonstrated that the testes were not atrophied and did not show chromosome pairing errors.ConclusionBased on the low genetic distance (which configures intraspecific variation), associated with the absence of prezygotic and postzygotic reproductive barriers, we confirm thatT. sordidaLa Paz represents only a chromosomal polymorphism ofT. sordidas.s.Graphical abstract
Increased risk of malignancy in patients with systemic lupus erythematosus: population-based cohort study in Korea
Authors: Han Jung-Yong , Kim Hyoungyoung , Jung Sun-Young , Jang Eun Jin , Cho Soo-Kyung , Sung Yoon-Kyoung 
Published: October 2021

Abstract
Background
This study aimed to evaluate the crude incidence rates and relative risk of malignancy in Korean patients with SLE.

Methods
We conducted a retrospective nationwide cohort study using databases from the National Health Insurance Service in Korea. All prevalent SLE patients aged over 19 were identified from January 2012 to December 2014 and observed until the diagnosis of malignancy, death, or end of the study, December 2015. The crude incidence rates (IRs) and standardised incidence ratios (SIRs) of overall and site-specific malignancies in SLE patients were estimated.

Results
We identified 17,854 SLE patients and during the observation period (60,511 person-years [PYs]), 768 solid malignancies (126.9/10,000 PYs) and 68 haematologic malignancies (11.2/10,000 PYs) occurred in SLE patients. In SLE patients, breast and reproductive system and thyroid cancers occurred predominantly, followed by liver and colon cancers. The SIRs of overall, solid, and haematologic malignancies of SLE patients compared to the general population were 1.8 (95% confidence interval [CI] 1.6–1.9), 1.7 (95% CI 1.5–1.8), and 5.9 (95% CI 4.8–7.3), respectively. In solid malignancies, head and neck (2.7, 95% CI 1.1–4.2), bladder (2.4, 95% CI 1.1–3.8), liver (1.9, 95% CI 1.4–2.3), pancreas (1.9, 95% CI 1.3–2.6), lung (1.8, 95% CI 1.2–2.4), colon (1.7, 95% CI 1.3–2.2), thyroid (1.6, 95% CI 1.3–1.8) and breast and reproductive system (1.5, 95% CI 1.2–1.7) cancers are at increased risk in SLE patients.

Conclusion
An increased risk of haematologic and solid malignancies was observed in Korean patients with SLE compared to the general population.
HIV incidence among men who have sex with men in mainland China: a systematic review protocol
Authors: Huang Wenting , Wang Liming , Guodong Mi , Zahn Ryan J. , Taussig Jennifer , Peterson Shenita R. , Baral Stefan , Moore Renee H. , Huang Xiaojie , Hou Jianhua , Sullivan Patrick S. , Siegler Aaron J. 
Published: October 2021

Abstract
Background
Men who have sex with men (MSM) are disproportionately affected by HIV in China. Globally, younger MSM are at higher risk for incident HIV infections, but there has been substantial variation in the estimates of age-stratified HIV incidence among MSM in mainland China, potentially due to regional differences in the nature of the epidemic. Given the need for quality epidemiological data to meet the global goal of ending new HIV infections by 2030, this systematic review and meta-analysis aims to determine age-stratified HIV incidence in mainland China, including consideration by geographic region and time.

Methods
This review will include longitudinal studies, cross-sectional surveys, and surveillance reports among MSM in mainland China that have reported HIV incidence. We will search studies and reports published from January 1, 2003, to April 30, 2020, in both English and Chinese language literature databases. For each study considered, two reviewers will independently screen, determine eligibility, and extract relevant data, with discrepancies resolved by consensus of a third reviewer. The methodological quality of included studies will be assessed by the Quality Assessment Tool for Systematic Reviews of Observational Studies Score (QATSO). We will develop age-stratified estimates of HIV incidence with geographic variations and temporal trends. Heterogeneity will be examined using statistical techniques appropriate to the dataset. For subgroup analyses, we will conduct mixed-effects meta-analysis models.

Discussion
This review will contribute to a better understanding of the HIV epidemic among MSM in mainland China by providing age-stratified estimates of HIV incidence with a portrayal of geographic and temporal variations. Findings will reflect epidemic dynamics, informing local and national intervention programs and policies for HIV prevention, and providing estimation data to inform future research among MSM in China.

Systematic review registration
PROSPERO ID 154834
Paediatric tuberculosis diagnosis using Mycobacterium tuberculosis real-time polymerase chain reaction assay: a systematic review and meta-analysis
Authors: Babafemi Emmanuel Oladipo , Cherian Benny P. , Ouma Beatrice , Mogoko Gilbert Mangua 
Published: October 2021

Abstract
Background
Rapid and accurate diagnosis of paediatric tuberculosis (TB) is key to manage the disease and to control and prevent its transmission. Collection of quality sputum samples without invasion methods from paediatrics (age < 16 years) with presumptive pulmonary tuberculosis (PTB) remains a challenge. Thus, the aim of this meta-analysis was to assess the overall accuracy of a real-time polymerase chain reaction (RT-PCR)-based assay, for routine diagnosis of MTB in different samples from paediatrics with active pulmonary and extra-pulmonary tuberculosis using mycobacterial culture as the gold standard in clinical microbiology laboratories.

Methods
We conducted a systematic review and meta-analysis to examine the diagnostic test accuracy of RT-PCR based assay for the detection of MTB in paediatric clinical samples.
A systematic literature search was performed for publications in any language. MEDLINE via PubMed, EMBASE, and Web of Science were among 9 bibliographic databases searched from August 2019 until November 2020. Bivariate random-effects model of meta-analysis were performed to generate pooled summary estimates (95% CIs) for overall accuracy of RT-PCR based assay compared to mycobacterial culture as the reference standard.

Results
Of the 1592 candidate studies, twenty-one eligible studies met our inclusion criteria. In total, the review and meta-analysis included 5536 (3209 PTB and 2327 EPTB). Summary estimates for pulmonary TB (11 studies) were as follows: sensitivity 56 (95% CI 51–62), specificity 97 (95% CI 96–98) and summary estimates for extra-pulmonary TB (10 studies) were as follows: sensitivity 87 (95% CI 82-91)) specificity 100 (95% CI 99–100). There was significant heterogeneity in sensitivity and specificity among the enrolled studies (p < 0.001).

Conclusions
Our results suggested that the RT-PCR based assay could be a useful test for the diagnosis of paediatrics TB with high sensitivity and specificity in low-income/high-burden and upper medium income/low-burden settings. From the study, RT-PCR assay demonstrated a high degree of sensitivity for extra-pulmonary TB and good sensitivity for pulmonary TB which is an important factor in achieving effective global control and for patient management in terms of initiating early and appropriate anti-tubercular therapy.

Systematic review registration
PROSPERO CRD42018104052
A survey on missing data in machine learning
Authors: Emmanuel Tlamelo , Maupong Thabiso , Mpoeleng Dimane , Semong Thabo , Mphago Banyatsang , Tabona Oteng 
Published: October 2021

AbstractMachine learning has been the corner stone in analysing and extracting information from data and often a problem of missing values is encountered. Missing values occur because of various factors like missing completely at random, missing at random or missing not at random. All these may result from system malfunction during data collection or human error during data pre-processing. Nevertheless, it is important to deal with missing values before analysing data since ignoring or omitting missing values may result in biased or misinformed analysis. In literature there have been several proposals for handling missing values. In this paper, we aggregate some of the literature on missing data particularly focusing on machine learning techniques. We also give insight on how the machine learning approaches work by highlighting the key features of missing values imputation techniques, how they perform, their limitations and the kind of data they are most suitable for. We propose and evaluate two methods, the k nearest neighbor and an iterative imputation method (missForest) based on the random forest algorithm. Evaluation is performed on the Iris and novel power plant fan data with induced missing values at missingness rate of 5% to 20%. We show that both missForest and the k nearest neighbor can successfully handle missing values and offer some possible future research direction.
Three-dimensional printed polylactic acid scaffold integrated with BMP-2 laden hydrogel for precise bone regeneration
Authors: Cha Misun , Jin Yuan-Zhe , Park Jin Wook , Lee Kyung Mee , Han Shi Huan , Choi Byung Sun , Lee Jae Hyup 
Published: October 2021

Abstract

Background
Critical bone defects remain challenges for clinicians, which cannot heal spontaneously and require medical intervention. Following the development of three-dimensional (3D) printing technology is widely used in bone tissue engineering for its outstanding customizability. The 3D printed scaffolds were usually accompanied with growth factors, such as bone morphometric protein 2 (BMP-2), whose effects have been widely investigated on bone regeneration. We previously fabricated and investigated the effect of a polylactic acid (PLA) cage/Biogel scaffold as a carrier of BMP-2. In this study, we furtherly investigated the effect of another shape of PLA cage/Biogel scaffold as a carrier of BMP-2 in a rat calvaria defect model and an ectopic ossification (EO) model.

Method
The PLA scaffold was printed with a basic commercial 3D printer, and the PLA scaffold was combined with gelatin and alginate-based Biogel and BMP-2 to induce bone regeneration. The experimental groups were divided into PLA scaffold, PLA scaffold with Biogel, PLA scaffold filled with BMP-2, and PLA scaffold with Biogel and BMP-2 and were tested both in vitro and in vivo. One-way ANOVA with Bonferroni post-hoc analysis was used to determine whether statistically significant difference exists between groups.

Result
The in vitro results showed the cage/Biogel scaffold released BMP-2 with an initial burst release and followed by a sustained slow-release pattern. The released BMP-2 maintained its osteoinductivity for at least 14 days. The in vivo results showed the cage/Biogel/BMP-2 group had the highest bone regeneration in the rat calvarial defect model and EO model. Especially, the bone regenerated more regularly in the EO model at the implanted sites, which indicated the cage/Biogel had an outstanding ability to control the shape of regenerated bone.

Conclusion
In conclusion, the 3D printed PLA cage/Biogel scaffold system was proved to be a proper carrier for BMP-2 that induced significant bone regeneration and induced bone formation following the designed shape.
High-resolution dynamic mapping of the C. elegans intestinal brush border
Authors: Bidaud-Meynard Aurélien , Demouchy Flora , Nicolle Ophélie , Pacquelet Anne , Suman Shashi Kumar , Plancke Camille N. , Robin François B. , Michaux Grégoire 
Published: October 2021

ABSTRACT
The intestinal brush border is made of an array of microvilli that increases the membrane surface area for nutrient processing, absorption and host defense. Studies on mammalian cultured epithelial cells have uncovered some of the molecular players and physical constraints required to establish this apical specialized membrane. However, the building and maintenance of a brush border in vivo has not yet been investigated in detail. Here, we combined super-resolution imaging, transmission electron microscopy and genome editing in the developing nematode Caenorhabditis elegans to build a high-resolution and dynamic localization map of known and new brush border markers. Notably, we show that microvilli components are dynamically enriched at the apical membrane during microvilli outgrowth and maturation, but become highly stable once microvilli are built. This new toolbox will be instrumental for understanding the molecular processes of microvilli growth and maintenance in vivo, as well as the effect of genetic perturbations, notably in the context of disorders affecting brush border integrity.
Syntaxin 17, an ancient SNARE paralog, plays different and conserved roles in different organisms
Authors: Kato Shun , Arasaki Kohei , Tokutomi Natsuki , Imai Yuzuru , Inoshita Tsuyoshi , Hattori Nobutaka , Sasaki Taeko , Sato Miyuki , Wakana Yuichi , Inoue Hiroki , Tagaya Mitsuo 
Published: October 2021

ABSTRACT
Mammalian syntaxin 17 (Stx17) has several roles in processes other than membrane fusion, including in mitochondrial division, autophagosome formation and lipid droplet expansion. In contrast to conventional syntaxins, Stx17 has a long C-terminal hydrophobic region with a hairpin-like structure flanked by a basic amino acid-enriched C-terminal tail. Although Stx17 is one of the six ancient SNAREs and is present in diverse eukaryotic organisms, it has been lost in multiple lineages during evolution. In the present study, we compared the localization and function of fly and nematode Stx17s expressed in HeLa cells with those of human Stx17. We found that fly Stx17 predominantly localizes to the cytosol and mediates autophagy, but not mitochondrial division. Nematode Stx17, on the other hand, is predominantly present in mitochondria and facilitates mitochondrial division, but is irrelevant to autophagy. These differences are likely due to different structures in the C-terminal tail. Non-participation of fly Stx17 and nematode Stx17 in mitochondrial division and autophagy, respectively, was demonstrated in individual organisms. Our results provide an insight into the evolution of Stx17 in metazoa.
This article has an associated First Person interview with the first author of the paper.