bluuebunny/crossref_metadata_2025 huggingface dataset:
Sugar Beet Root Storage Properties Are Unaffected by Cercospora Leaf Spot
Authors: Fugate Karen K. , Khan Mohamad F. R. , Eide John D. , Hakk Peter C. , Lafta Abbas M. , Qi Aiming
Published: November 2022

Cercospora leaf spot (CLS; causal agent Cercospora beticola Sacc.) is endemic in many sugar beet production regions due to the widespread distribution of C. beticola and the inability of current management practices to provide complete control of the disease. Roots harvested from plants with CLS, therefore, are inevitably incorporated into sugar beet root storage piles, even though the effects of CLS on root storage properties are largely unknown. Research was conducted to determine the effects of CLS on storage properties including root respiration rate, sucrose loss, invert sugar accumulation, loss in recoverable sucrose yield, and changes in sucrose loss to molasses with respect to CLS disease severity and storage duration. Roots were obtained from plants with four levels of CLS severity in each of three production years, stored at 5°C and 95% relative humidity for up to 120 days, and evaluated for storage characteristics after 30, 90, and 120 days storage. No significant or repeatable effects of CLS on root respiration rate, sucrose loss, invert sugar accumulation, loss in recoverable sucrose yield, or change in sucrose loss to molasses were detected after 30, 90, or 120 days storage regardless of the severity of CLS disease symptoms. Therefore, no evidence was found that CLS accelerates sugar beet storage losses, and it is concluded that roots harvested from plants with CLS can be stored without additional or specialized precaution, regardless of CLS symptom severity.
Addressing Self-Injurious Behavior in the Medically Complex Child: Identifying the Root Cause vs Blocking Resulting Behavior
Authors: Low Kapalu Christina , Krasaelap Amornluck , Nyp Sarah S.
Published: November 2022

CASE:

Gillian is a 7-year-old nonverbal, internationally adopted girl with significant visual impairment (sees shadows and objects with high contrast), moderate-severe hearing loss, autism spectrum disorder, profound intellectual disability, and a seizure disorder. She resided in an orphanage until age 4 years when she was adopted by her mother. She is referred to the multidisciplinary team in developmental-behavioral pediatrics by her gastroenterologist, who is managing her constipation, for evaluation and management of self-injurious behavior that occurs before bowel movements.

Gillian's adoptive mother reported that Gillian has a history of repetitive and self-injurious behavior including hitting her head with the palm of her hand and poking her eyes. The head-hitting behavior has resulted in consistent bruising to her forehead and nasal bridge. The eye poking is of significant concern because of the possibility of resultant injury including corneal abrasion or retinal detachment. Eye poking occurs exclusively during the hour before stooling, at home and school, and is accompanied by screaming, pacing, and increased aggression toward her mother/teachers. Mother typically responds by blocking the eye poking, redirecting Gillian to the toilet, providing prompts to use calming strategies (e.g., deep breathing), or providing sensory input by rubbing her arms/back. Teachers respond in a similar way at school. Gillian's mother has tried to place goggles over Gillian's eyes during eye poking, but this resulted in increased aggressive behaviors.

Gillian is not fully bowel trained but will sit on the toilet to urinate when prompted. She completes toilet-sits at home/school 5 to 7 times daily. Gillian passes small, soft bowel movements 2 to 4 times daily on a bowel management regimen consisting of polyethylene glycol 3350 17 grams twice daily and liquid senna 8.8 mg daily. Seizures are reportedly well controlled with an antiepileptic medication managed by her neurologist. Previous medical evaluation by otolaryngology, ophthalmology, neurology, and gastroenterology did not identify a source of pain or other cause for the eye poking. Physical examination reveals normal bowel sounds and a mildly distended abdomen but is otherwise unremarkable. What are your next steps for evaluation and treatment?
Evaluation of Chronic Constipation in Children With Autism Spectrum Disorder
Authors: Coe Alexander , Ciricillo Jacob , Mansi Sherief , El-Chammas Khalil , Santucci Neha , Bali Neetu , Lu Peter L. , Damrongmanee Alisara , Fei Lin , Liu Chunyan , Kaul Ajay , Williams Kent C.
Published: November 2022

Objectives:

Chronic constipation occurs frequently in children with autism spectrum disorder (ASD). The primary objective was to determine whether chronic constipation is associated with a higher rate of abnormal colonic motor activity in ASD children than in non-ASD children. A secondary goal was to determine if clinical variables could identify children with ASD at risk for possessing abnormal colonic motility.

Methods:

A retrospective, propensity-matched, case-control study compared colonic manometry (CM) of an ASD cohort and non-ASD controls with chronic constipation. Clinical variables were evaluated as potential predictors for abnormal colonic motility.

Results:

Fifty-six patients with ASD and 123 controls without the diagnosis of ASD who underwent CM were included. Propensity score resulted in 35 matched cohorts of ASD and controls. The rate of abnormal CM findings between ASD and matched controls (24% vs 20%, P = 0.78) did not differ significantly. A prediction model of abnormal CM that included ASD diagnosis, duration of constipation, and soiling achieved a sensitivity of 0.94 and specificity of 0.65. The risk for abnormal colonic motility increased 11% for every 1-year increase in duration of constipation. Odds for abnormal motility were 30 times higher in ASD children with soiling than controls with soiling (P < 0.0001).

Conclusions:

Chronic constipation does not appear to be associated with a higher rate of abnormal colonic motility in children with ASD. Clinical information of disease duration and presence of soiling due to constipation show promise in identifying patients with ASD at a greater risk for abnormal colonic motility.
An Education Intervention to Raise Awareness Reduces Self-reported Opioid Overprescribing by Plastic Surgery Residents
Authors: Skladman Rachel , Keane Grace C. , Grant David , Mackinnon Susan E.
Published: November 2022

Purpose

The aim of this study was to understand how opioid prescribing practices of plastic surgery residents changed after instituting opioid prescribing education (OPE) interventions.

Methods

Plastic surgery residents at a single academic institution completed a survey (fall 2017) assessing opioid prescribing following 8 common procedures. The Division then completed 3 multidisciplinary OPE interventions over 2.5 years, which provided passive learning to raise awareness without top-down prescribing guidelines. Residents were resurveyed at 2 time points after the interventions (fall 2018 and spring 2020). The primary outcome measure was self-reported morphine milligram equivalents prescribed.

Results

Survey response rates were 84% to 100%. Preintervention opioid prescriptions were characterized by high variability and absolute doses for all procedures. We observed statistically significant decreases in prescribed doses for most procedures at 9 months post intervention and further decreases at 2.5 years. In the most recently surveyed cohort, only 3 of 16 residents (18.8%) had OPE before residency, whereas 12 of 16 residents (75.0%) participated in OPE during residency. Eighty-eight percent of respondents “always” (8/16, 50%) or “usually” (6/16, 38%) considered the opioid epidemic when prescribing opioids, suggesting an improved prescribing culture. Barriers to better prescribing included duplicate prescriptions/accessing state-run prescription drug monitoring programs (75.0%), remote prescribing (75%), providing refills (56%), and prescribing opioids for patients on chronic opioid therapy (56%).

Conclusion

This prospective cohort study demonstrates that a simple multidisciplinary, didactic OPE intervention that aimed to increase residents' awareness has the potential to reduce self-reported opioid prescribing and sustain prescribing practices over many years. We identify persistent barriers facing our resident prescribers today, enabling more opioid educational interventions in the future.
Comparison of the Relapse Ratio and Osteogenesis Between 1-Piece and 2-Piece Fronto-Orbital Distraction Osteogenesis Among Patients With Bilateral Craniosynostosis in Early Childhood
Authors: Park Hojin , Choi Jong Woo , Ra Young Shin
Published: November 2022

Background

Fronto-orbital distraction osteogenesis (FODO), used to correct bilateral coronal craniosynostosis (BCS), is grossly classified into 1-piece and 2-piece FODO. One-piece FODO osteomizes the frontal and supraorbital bones as one block by preserving the attachment between the dura mater and bone, whereas the 2-piece FODO detaches bone segments from the underlying dura mater and reshapes them. This study aimed to determine whether separating the bone-dura attachment would affect osteogenesis and the relapse of the deformity and to compare the surgical outcomes between 1-piece and 2-piece FODO.

Methods

Patients with BCS who underwent either 1-piece or 2-piece FODO between May 2008 and November 2016 were retrospectively reviewed. Patients older than 12 months who were diagnosed with syndromic or nonsyndromic craniosynostosis were included. The CT images were taken at initial presentation (T0), 1–3 years postoperatively (T1), and >4 years postoperatively (T2). These images were used to measure the frontal angle, anterior skull base ratio, and bone defect area.

Results

This study included 11 patients in the 1-piece group and 9 patients in the 2-piece group. The relapse ratios of the frontal angle were −2.3% ± 0.6% and −4.9% ± 2.1% in the 1-piece and 2-piece groups, respectively, showing that the 2-piece group had a significantly higher relapse ratio (P = 0.002). At the T2 period, the 1-piece group had a significantly higher anterior skull base ratio (0.80 ± 0.10) than that in the 2-piece group (0.69 ± 0.08, P = 0.046). In addition, the bone defect area was significantly lower in the 1-piece group (T1: 4.90 ± 2.32 cm2, T2: 2.55 ± 1.57 cm2) than in the 2-piece group (T1: 10.74 ± 5.89 cm2, T2: 5.35 ± 2.74 cm2) both at the T1 (P = 0.037) and T2 (P = 0.025) periods.

Conclusions

One-piece FODO can result in the preservation of the bone segments' vascularity and the enhancement of osteogenesis in the distraction gap. Moreover, 1-piece FODO is associated with lower rates of relapse of deformity and bone defects compared with 2-piece FODO. Lastly, 1-piece FODO can be performed to maximize the advantages of distraction osteogenesis and improve surgical outcomes, especially among early childhood patients with BCS.
High-Quality Lipoaspirate Following 1470-nm Radial Emitting Laser-Assisted Liposuction
Authors: Shapira Eyal , Plonski Lori , Menashe Shaked , Ofek Andre , Rosenthal Adaya , Brambilla Massimiliano , Goldenberg Gary , Haimowitz Sahar , Heller Lior
Published: November 2022

Background

Laser-assisted liposuction (LAL) has been used to maximize viable adipocyte yields in lipoaspirates, although optimizing tissue processing methods is still a challenge. A high-quality lipoaspirate has been a key factor for extended graft longevity.

Objective

To assess the viability and potency of stromal vascular fraction (SVF) cells and adipose-derived stem cells (ASCs) in fat samples from lipoaspirates harvested with a novel 1470-nm diode, radial emitting LAL platform. Two processing methods, enzymatic and nonenzymatic, were compared.

Methods

Laser-assisted liposuction lipoaspirates harvested from 10 subjects were examined for cell viability after processing by enzymatic or nonenzymatic methods. Isolated SVF cells were cultured with an ASC-permissive medium to assess their viability and proliferation capacity by cell proliferation assay. Flow cytometric analysis with ASC-specific markers, gene expression levels, and immunofluorescence for ASC transcription factors were also conducted.

Results

Lipoaspirates showed high SVF cell viability of 97% ± 0.02% and 98% ± 0.01%, averaged SVF cell count of 8.7 × 106 ± 3.9 × 106 and 9.4 × 106 ± 4.2 × 106 cells per mL, and averaged ASC count of 1 × 106 ± 2.2 × 105 and 1.2 × 106 ± 5 × 105 cells per mL in nonenzymatic and enzymatic methods, respectively. The ASC-specific markers, gene expression levels, and immunofluorescence for ASC transcription factors confirmed the adipose origin of the cells.

Conclusions

The laser lipoaspirates provide a high yield of viable and potent SVF cells and ASCs through both nonenzymatic and enzymatic processes. Improved purity of the harvested lipoaspirate and high ASC content are expected to result in extended graft longevity. Furthermore, eliminating enzymatic digestion may provide advantages, such as reducing process time, cost, and regulatory constraints.
Comparison of Human, Porcine, and Bovine Acellular Dermal Matrix in Prepectoral Breast Reconstruction
Authors: Pires Giovanna R. , Moss Whitney D. , Hosein Ray C. , Overschmidt Bo T. , Magno-Padron David A. , Agarwal Jayant P. , McFarland Mary M. , Casucci Tallie , Kwok Alvin C.
Published: November 2022

Objective

The aim of the study is to determine rates of overall complications and failure of prepectoral breast reconstruction between various types of acellular dermal matrices (ADMs).

Background

Implant-based breast reconstruction is the most common reconstructive technique after mastectomy in the United States. Traditionally, the reconstruction has been performed in the subpectoral plane; however, there has been an emerging interest in prepectoral reconstruction using ADM. Human (hADM), porcine (pADM), and bovine (bADM) ADMs are available for use, but little is known about the benefits and complication profiles of each for prepectoral breast reconstruction.

Methods

Studies examining complications after the use of ADM for prepectoral breast reconstruction were identified using MEDLINE, Embase, the Cochrane Library, LILACS, and the Web of Science from January 2010 to August 2021. Titles and abstracts of 1838 studies were screened, followed by full-text screening of 355 articles. Thirty-three studies were found to meet inclusion criteria.

Results

From the 33 studies, 6046 prepectoral reconstructions were examined. Implant loss was comparable across the different types of ADM (pADM, 4.0%; hADM, 4.0%; bADM, 3.7%). Bovine ADM had the highest rate of capsular contracture (6.1%), infection (9.0%), skin flap necrosis (8.3%), dehiscence (5.4%), and hematoma (6.1%) when compared with both hADM and pADM. Human ADM had the highest rate of postoperative seroma (5.3%), followed by pADM (4.6%) and bADM (4.5%).

Conclusions

Among the prepectoral breast reconstruction studies using hADM, pADM, or bADM included in our analysis, complication profiles were similar. Bovine ADM had the highest proportion of breast complications in the following categories: capsular contracture, infection rate, skin flap necrosis, dehiscence, and hematoma. Implant loss was comparable across the cohorts. Overall, prepectoral breast reconstruction using ADM leads to relatively low complication rates with the highest rates within the bADM cohort.
Risk Factors Associated With Pressure Injuries in Surgical Patients
Authors: Kim Jung Yoon , Lee Hyun Hee
Published: November 2022

PURPOSE:

This study aimed to identify predictive risk factors for pressure injury (PI) occurring during surgery.

DESIGN:

Retrospective case-control study.

SUBJECTS AND SETTING:

Data on records of 6070 patients hospitalized for surgery at Seoul National University Bundang Hospital located in Seoul Korea. Data were collected between May 2013 and December 2014.

METHODS:

Anonymized data from patients were accessed via electronic health records, nursing records, direct patient assessment, surgical, clinical laboratory, and anesthesia records, preanesthesia status evaluations, and PI incident reports, and transfusion and extracorporeal circulation reports. Descriptive and logistic regression analyses were conducted.

RESULTS:

Three hundred eighty-one of the 6070 patients (6.3%) developed within 24 hours a PI that was associated with surgery. The most common locations for the PIs were the coccyx (15.1%; n = 75) and trunk (chest or abdomen; 15.1%; n = 75). All PIs were classified as stage 1 (66.6%; n = 331) or 2 (33.4%; n = 166). Based on logistic regression results, we found that the risk factors that were independently predictive of surgery-related PIs were patient position during surgery, admission to an intensive care unit after surgery, required blood transfusion during surgery, and duration of surgery.

CONCLUSIONS:

This retrospective study identified several risk factors associated with a higher incidence of perioperative PIs in surgical patients. A PI prevention program accounting for these factors could potentially help prevent PIs and their costly complications.
Cytokinetic diversity in mammalian cells is revealed by the characterization of endogenous anillin, Ect2 and RhoA
Authors: Husser Mathieu C. , Ozugergin Imge , Resta Tiziana , Martin Vincent J. J. , Piekny Alisa J.
Published: November 2022

Cytokinesis is required to physically separate the daughter cells at the end of mitosis. This crucial process requires the assembly and ingression of an actomyosin ring, which must occur with high fidelity to avoid aneuploidy and cell fate changes. Most of our knowledge of mammalian cytokinesis was generated using over-expressed transgenes in HeLa cells. Over-expression can introduce artefacts, while HeLa are cancerous human cells that have lost their epithelial identity, and the mechanisms controlling cytokinesis in these cells could be vastly different from other cell types. Here, we tagged endogenous anillin, Ect2 and RhoA with mNeonGreen and characterized their localization during cytokinesis for the first time in live human cells. Comparing anillin localization in multiple cell types revealed cytokinetic diversity with differences in the duration and symmetry of ring closure, and the timing of cortical recruitment. Our findings show that the breadth of anillin correlates with the rate of ring closure, and support models where cell size or ploidy affects the cortical organization, and intrinsic mechanisms control the symmetry of ring closure. This work highlights the need to study cytokinesis in more diverse cell types, which will be facilitated by the reagents generated for this study.
How neutrophil metabolism affects bacterial killing
Authors: Toller-Kawahisa Juliana E. , O'Neill Luke A. J.
Published: November 2022

Neutrophils are front line cells in immunity that quickly recognize and eliminate pathogens, relying mainly on glycolysis to exert their killing functions. Even though investigations into the influence of metabolic pathways in neutrophil function started in the 1930s, the knowledge of how neutrophils metabolically adapt during a bacterial infection remains poorly understood. In this review, we discuss the current knowledge about the metabolic regulation underlying neutrophils response to bacterial infection. Glycogen metabolism has been shown to be important for multiple neutrophil functions. The potential contribution of metabolic pathways other than glycolysis, such as mitochondrial metabolism, for neutrophil function has recently been explored, including fatty acid oxidation in neutrophil differentiation. Complex III in the mitochondria might also control glycolysis via glycerol-3-phosphate oxidation. Future studies should yield new insights into the role of metabolic change in the anti-bacterial response in neutrophils.
The role of α-sheet structure in amyloidogenesis: characterization and implications
Authors: Prosswimmer Tatum , Daggett Valerie
Published: November 2022

Amyloid diseases are linked to protein misfolding whereby the amyloidogenic protein undergoes a conformational change, aggregates and eventually forms amyloid fibrils. While the amyloid fibrils and plaques are hallmarks of these diseases, they typically form late in the disease process and do not correlate with disease. Instead, there is growing evidence that smaller, soluble toxic oligomers form prior and appear to be early triggers of the molecular pathology underlying these diseases. Nearly 20 years ago, we proposed the α-sheet hypothesis after discovering that the early conformational changes observed during atomistic molecular dynamics simulations involve the formation of a non-standard protein structure, α-sheet. Furthermore, we proposed that toxic oligomers contain α-sheet structure and that preferentially targeting this structure could neutralize the toxicity, prevent further aggregation and serve as the basis for early detection of disease. Here, we present the origin of the α-sheet hypothesis and describe α-sheet structure and the corresponding mechanisms of conversion. We discuss experimental studies demonstrating that both mammalian and bacterial amyloid systems form α-sheet oligomers before converting to conventional β-sheet fibrils. Furthermore, we show that the process can be inhibited withde novodesigned α-sheet peptides complementary to the structure in the toxic oligomers.
Temperature shifts associated with bat arousals during hibernation inhibit the growth of
Pseudogymnoascus destructans
Authors: Forney Ronny , Rios-Sotelo Gabriela , Lindauer Alexa , Willis Craig K. R. , Voyles Jamie
Published: November 2022

Temperature is a critically important factor in many infectious disease systems, because it can regulate responses in both the host and the pathogen. White-nose syndrome (WNS) in bats is a severe infectious disease caused by the temperature-sensitive fungus,
Pseudogymnoascus destructans
(
Pd
). One feature of WNS is an increase in the frequency of arousal bouts (i.e. when bat body temperatures are elevated) in
Pd
-infected bats during hibernation. While several studies have proposed that increased frequency of arousals may play a role in the pathophysiology of WNS, it is unknown if the temperature fluctuations might mediate
Pd
growth. We hypothesized that exposure to a high frequency of elevated temperatures would reduce
Pd
growth due to thermal constraints on the pathogen. We simulated the thermal conditions for arousal bouts of uninfected and infected bats during hibernation (fluctuating from 8 to 25°C at two different rates) and quantified
Pd
growth
in vitro
. We found that increased exposure to high temperatures significantly reduced
Pd
growth. Because temperature is one of the most critical abiotic factors mediating host–pathogen interactions, resolving how
Pd
responds to fluctuating temperatures will provide insights for understanding WNS in bats and other fungal diseases.
Generalized tendency to make extreme trait judgements from faces
Authors: Suzuki Atsunobu , Tsukamoto Saori , Takahashi Yusuke
Published: November 2022

People differ in their tendency to infer others' personalities and abilities from their faces. An extreme form of such face-based trait inference (FBTI) is problematic because of its unwarranted impact on real-world decision making. Evolutionary perspectives on FBTI suggest that its inter-individual variation would be
trait-specific
: e.g. those who make extreme face-based inferences about trustworthiness may not necessarily do so about dominance. However, there are several psychological variables that can increase the FBTI extremity across traits. Here, we show that there is a generalized individual tendency to make extreme FBTI across traits, in support of the latter view. We found that the degrees of extremity of face-based inferences about seven traits had high cross-trait correlations, constituting a general factor. This
generalized FBTI extremity
had good test–retest reliability and was neither an artefact of extreme nor socially desirable response biases. Moreover, it was positively associated with facial emotion recognition ability and tendencies to believe physiognomy and endorse stereotypes. Our results demonstrate that there are individuals who have a temporally stable disposition to draw extreme conclusions about various traits of others from facial appearance as well as their psychological characteristics.
Enhanced durability of round bamboo treated with copper naphthenate under heat-cold impregnation
Authors: Jiang Jun , Han Shuaibo , Ren Xin , Wang Hui , Yu Hongwei , Sun Fangli
Published: November 2022

Round bamboo has aroused much interest in construction for its mechanical properties, but poor biological durability seriously restricts its application. In order to develop a suitable and effective preservative treatment method for round bamboo, copper naphthenate (CuN) was adopted and impregnated into round bamboo using heat-cold procedure. The distribution and retention of copper naphthenate in round bamboo were studied, and the biological durability represented by the mould and decay resistance were investigated. The results showed that the retention and fixation of copper reached 0.39 kg⋅m
−3
and 85.3%, respectively. Scanning electron microscopy–energy dispersive X-ray spectrometry further disclosed an increasing trend in the composition of CuN from the end inward. X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy analyses later revealed that CuN could be fixed on bamboo in the form of hydrogen bond or complex reaction. Statistical analysis showed that the increasing concentration of CuN from 0.3% to 0.5% and 0.8% (calculated as Cu
2+
content) has significant contribution against
Trametes versicolor
and
Gloeophyllum trabeum
in comparison with the untreated bamboo. Meanwhile, when the concentration of treating solution increased to 0.8 wt%, the resisting efficacy for
Aspergillus niger
,
Penicillium citrinum
and
Trichoderma viride
soared as high as 85.9%, 94.8% and 70.3%, respectively.
Can genomic research make a useful contribution to social policy?
Authors: Asbury Kathryn , McBride Tom , Bawn Rosie
Published: November 2022

As genetic research into outcomes beyond health gathers pace, largely through the use of genome-wide association studies, interest from policy-makers has grown. In the last year, two UK reports have explored the policy implications of genomic research, one from the UK Government Office for Science and one from the Early Intervention Foundation. In this article, we explore areas of consensus between these two reports and use them to propose priorities for policy-makers as we prepare for what some have termed a ‘genetic revolution’. Both reports agree on two clear recommendations for science and policy communities. One of these relates to public education and engagement, and the other to ensuring that genomic databases are ancestrally diverse. Both reports agree that—even if it is found to be a viable and ethical idea in the medium-term future—DNA data should not be incorporated into social policy before these two issues have been comprehensively addressed. In the article, we argue that scientists are taking the lead on tackling the diversity deficit but that there is a clear role for policy-makers to play in addressing low genetic literacy in society, and that this is a matter of urgency.
Complete genome and pathogenesis of a novel recombinant Senecavirus A isolate in P.R. China
Authors: Li Chen , Wu Xiaoyan , Wang Xiaoli , Shi Jianli , Liu Chang , Peng Zhe , Han Hong , Xu Shaojian , Wang Shuo , Ma Yingru , Zheng Limei , Hrabchenko Nataliia , Li Jun
Published: November 2022

Senecavirus A (SVA), formerly called Seneca Valley virus (SVV) was first isolated from the USA in 2002. This study isolated an SVA strain from a pig herd in Shandong Province, PR China and designated it SVA-CH-SDGT-2017. The full-length genome, excluding the poly(A) tails of the SVA isolates, was 7280 nucleotides long, with the genomic organization resembling and sharing high nucleotide identities of 90.7–96.9 % with other previously reported SVA isolates. To investigate the pathogenicity of the SVA isolates, experimental infections of pigs were performed. The SVA strains successfully infected the pigs, as evidenced by the presence of virus shedding and robust serum neutralizing antibody responses. In addition, the contact-exposed experiment showed that the virus shedding of the contact-exposed pigs was approximately a 100-fold reduced compared to that of the inoculated group, indicating that the virus is capable of transmission to pigs. Our findings provide useful data for studying the pathogenesis and transmission of SVA in pigs.
Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing
Authors: Hijikata Atsushi , Suyama Mikita , Kikugawa Shingo , Matoba Ryo , Naruto Takuya , Enomoto Yumi , Kurosawa Kenji , Harada Naoki , Yanagi Kumiko , Kaname Tadashi , Miyako Keisuke , Takazawa Masaki , Sasai Hideo , Hosokawa Junichi , Itoga Sakae , Yamaguchi Tomomi , Kosho Tomoki , Matsubara Keiko , Kuroki Yoko , Fukami Maki , Adachi Kaori , Nanba Eiji , Tsuchida Naomi , Uchiyama Yuri , Matsumoto Naomichi , Nishimura Kunihiro , Ohara Osamu
Published: November 2022

Next-generation DNA sequencing (NGS) in short-read mode has been recently used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, focusing mostly on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains mostly unexplored despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions using 10 genome sequence features on the basis of real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). We used the obtained metrics, designated “UNMET score,” along with other lines of structural information of the human genome to identify difficult-to-sequence genomic regions using conventional NGS. Thus, the UNMET score could provide appropriate caveats to address potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.
Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria
Authors: Dolcemascolo Roswitha , Heras-Hernández María , Goiriz Lucas , Montagud-Martínez Roser , Requena-Menéndez Alejandro , Ruiz Raúl , Pérez-Ràfols Anna , Higuera-Rodríguez R. Anahí , Pérez-Ropero Guillermo , Vranken Wim F. , Martelli Tommaso , Kaiser Wolfgang , Buijs Jos , Rodrigo Guillermo
Published: November 2022

The RNA recognition motif (RRM) is the most common RNA-binding protein domain identified in nature. However, RRM-containing proteins are only prevalent in eukaryotic phyla, in which they play central regulatory roles. Here, we engineered an orthogonal post-transcriptional control system of gene expression in the bacteriumEscherichia coliwith the mammalian RNA-binding protein Musashi-1, which is a stem cell marker with neurodevelopmental role that contains two canonical RRMs. In the circuit, Musashi-1 is regulated transcriptionally and works as an allosteric translation repressor thanks to a specific interaction with the N-terminal coding region of a messenger RNA and its structural plasticity to respond to fatty acids. We fully characterized the genetic system at the population and single-cell levels showing a significant fold change in reporter expression, and the underlying molecular mechanism by assessing thein vitrobinding kinetics andin vivofunctionality of a series of RNA mutants. The dynamic response of the system was well recapitulated by a bottom-up mathematical model. Moreover, we applied the post-transcriptional mechanism engineered with Musashi-1 to specifically regulate a gene within an operon, to implement combinatorial regulation, and to reduce protein expression noise. This work illustrates how RRM-based regulation can be adapted to simple organisms, thereby adding a new regulatory layer in prokaryotes for translation control.
Measures to assess quality of postnatal care: a scoping review
Authors: Galle Anna , Moran Allisyn C , Bonet Mercedes , Graham Katriona , Muzigaba Moise , Portela Anayda , Day Louise Tina , Tuabu Godwin Kwaku , De Sá é Silva Bianca , Moller Ann-Beth
Published: November 2022

High quality postnatal care is key for the health and wellbeing of women after childbirth and their newborns. In 2022, the World Health Organization (WHO) published global recommendations on maternal and newborn care for a positive postnatal care experience. Evidence regarding appropriate measures to monitor implementation of postnatal care (PNC) according to the WHO recommendations is lacking. This scoping review aims to document the measures used to assess the quality of postnatal care and their validity. The review was conducted according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). Five electronic bibliographic databases were searched together with a grey literature search. Two reviewers independently screened and appraised identified articles. All data on PNC measures were extracted and mapped to the postnatal care guideline according to three categories: i) maternal care, ii) newborn care, iii) health system and health promotion interventions. We identified 62 resources providing measures aligning with the WHO PNC recommendations. For most PNC recommendations there were measures available and the highest number of recommendations were found for breastfeeding and the assessment of the newborn. No measures were found for recommendations related to sedentary behavior, criteria to be assessed before discharge, retention of staff in rural areas and use of digital communication. Measure validity assessment was described in 24 articles (39%), but methods were not standardized. Our study highlights a gap in existing PNC measures for several recommendations in the WHO PNC guideline. Assessment of the validity of measurement of PNC indicators was limited. Consensus on how the quality of PNC should be measured is needed, involving a selection of priority measures and the development of new measures as appropriate.
Predictors of long-term progression to chronic kidney disease in HIV infection in Ghana from 2003-2018
Authors: Chadwick David R , Barker Fred , Smith Colette , Perditer Okyere , Hardy Yasmine , Owusu Dorcas , Villa Giovanni , Sarfo Fred Stephen , Geretti Anna-Maria , Phillips Richard
Published: November 2022

Aim

HIV is associated with an increased risk of progression to chronic kidney disease (CKD), and this risk is higher in people of West African descent than many other ethnicities. Our study aimed to assess the rates of progression to CKD and predictors of rapid progression in patients receiving antiretroviral therapy (ART) in central Ghana between 2003 and 2018.

Methods

This single-centre retrospective study enrolled people with HIV (PWH) initiating ART in Ghana between 2003-2018. Demographics, hepatitis B (HBsAg) status, ART regimens and eGFR measurements were recorded, and multi-level model linear regression was performed to determine predictors of greater levels of eGFR decline.

Results

659 participants were included in the study with a median follow-up time of 6 years (IQR 3.6-8.9). 149 participants (22.6%) also had confirmed HBV co-infection. Tenofovir was associated with the highest mean rate of eGFR decline of all Nucleoside/Nucleotide Reverse Transcriptase Inhibitors (NRTIs), representing a statistically significant annual decline -1.08 mL/min/1.73m2/year (CI: -0.24, -1.92) faster than those taking zidovudine. Regarding other ARTs, both nevirapine (-0.78mL /min/173m2/year; CI: -0.17, -1.39) and protease inhibitors (-1.55mL/mil/173m2/year; CI: - 0.41, -2.68) were associated with slower eGFR declines compared with efavirenz. Negative HbsAg status was associated with greater eGFR decline compared with positive HBsAg status (-1.25mL/mil/173m2; CI 0.29. 2.20).

Conclusion

Increased rates of eGFR decline amongst PWH in Ghana were associated with tenofovir, nevirapine, and protease inhibitor use as well as negative HBsAg status. Further higher-quality research is needed to explore long-term predictors of eGFR decline in African populations.
Sequence type diversity amongst antibiotic-resistant bacterial strains is lower than amongst antibiotic-susceptible strains
Authors: Pradhananga Anjani , Benitez-Rivera Lorena , Clark Candace , Tisthammer Kaho , Pennings Pleuni Simone
Published: November 2022

The increasing number of antibiotic resistant bacterial infections is a global threat to human health. Antibiotic resistant bacterial strains generally evolve from susceptible strains by either horizontal gene transfer or chromosomal mutations. After evolving within a host, such resistant strains can be transmitted to other hosts and increase in frequency in the population at large. Population genetic theory postulates that the increase in frequency of an adaptive trait can lead to signatures of selective sweeps. One would thus expect to observe reduced genetic diversity amongst that part of the population that carries the adaptive trait. Specifically, if the evolution of new resistant strains is rare, it is expected that resistant strains represent only a subset of the diversity of susceptible strains. It is currently unknown if diversity of resistant strains is indeed lower than diversity of susceptible strains when considering antibiotic resistance. Here we show that in several bacterial species in several different datasets, sequence-type diversity amongst antibiotic-resistant bacterial strains is indeed lower than amongst antibiotic-susceptible strains in most cases. We re-analysed eight existing clinical datasets withEscherichia coli, Staphylococcus aureusandEnterococcus faeciumsamples. These datasets consisted of 53 - 1094 patient samples, with multi-locus sequence types and antibiotic resistance phenotypes for 3 - 19 different antibiotics. Out of 59 comparisons, we found that resistant strains were significantly less diverse than susceptible strains in 51 cases (86%). In addition, we show that sequence-type diversity of antibiotic-resistant strains is lower if resistance is rare, compared to when resistance is common, which is consistent with rare resistance being due to fewer evolutionary origins. Our results show that for several different bacterial species, we observe reduced diversity of resistant strains, which is consistent with the evolution of resistance driven by selective sweeps stemming from a limited number of evolutionary origins. In future studies, more detailed analysis of such sweep signatures is warranted.
MSdb: an integrated expression atlas of human musculoskeletal system
Authors: Lin Junxin , Tian Ruonan , Xue Ziwei , Ruan Dengfeng , Chen Pengwei , Xu Yiwen , Dai Chao , Shen Weiliang , Ouyang Hongwei , Liu Wanlu
Published: November 2022

We introduce MSdb (https://www.msdb.org.cn), a database for visualization and integrated analysis of next-generation sequencing data from human musculoskeletal system, along with manually curated patient phenotype data. Systematic categorizing, standardized processing and freely accessible knowledge enables the reuse of public data. MSdb provides various types of analysis, including sample-level browsing of metadata information, gene/miRNA expression, and single-cell RNA-seq dataset. In addition, MSdb also allows integrated analysis for cross-samples and cross-omics analysis, including customized differentially-expressed gene/microRNA analysis, microRNA-gene network, scRNA-seq cross-sample/disease integration, and gene regulatory network analysis.
Histo-blood Group Antigen status of Australian Aboriginal children and seropositivity following oral rotavirus vaccination
Authors: Middleton Bianca F. , Danchin Margie , Cunliffe Nigel A. , Jones Mark A. , Boniface Karen , Kirkwood Carl D. , Gallagher Sarah , Kirkham Lea-Ann , Granland Caitlyn , McNeal Monica , Donato Celeste , Bogdanovic-Sakran Nada , Handley Amanda , Bines Julie E. , Snelling Thomas L.
Published: November 2022

Background

High rates of breakthrough rotavirus gastroenteritis have been reported among Aboriginal children living in rural and remote Australia despite receipt of two doses of oral rotavirus vaccine. Histo-blood group antigens (HBGAs) may mediate rotavirus genotype-dependent differences in susceptibility to rotavirus infection and immune responses to rotavirus vaccination.

Methods

HBGA phenotype – Lewis and secretor status - was determined by enzyme immunoassay of saliva samples obtained from Australian Aboriginal children who were enrolled at age 6 to <12 months in a randomised clinical trial of an additional (booster) dose of oral rotavirus vaccine. Participants had received the routine two-dose schedule of oral rotavirus vaccine administered at age 6 weeks and 4 months. Non-secretor phenotype was confirmed by DNA extraction to identifyFUT2‘G428A’ mutation. Rotavirus seropositivity was defined as serum anti-rotavirus IgA ≥ 20 AU/mL measured by ELISA on enrolment.

Results

Of 156 children, 119 (76%) were secretors, 129 (83%) were Lewis antigen positive, and 105 (67%) were rotavirus IgA seropositive. Eighty-seven of 119 (73%) secretors were rotavirus seropositive, versus 4/9 (44%) weak secretors and 13/27 (48%) non-secretors. Eighty-nine of 129 (69%) Lewis antigen positive children were rotavirus seropositive versus 10 of 19 (53%) of those who were Lewis antigen negative.

Conclusions

Most Australian Aboriginal children were secretor and Lewis antigen positive. Non-secretor children were less likely to be seropositive for rotavirus following vaccination, but this phenotype was less common. HBGA status is unlikely to fully explain the underperformance of rotavirus vaccine at a population level among Australian Aboriginal children.
NasopharyngealStaphylococcus aureuscolonization among HIV-infected children in Addis Ababa, Ethiopia: Antimicrobial susceptibility pattern and association withStreptococcus pneumoniaecolonization
Authors: Gebre Henok Alemu , Wami Ashenafi Alemu , Kebede Eyerusalem Solomon , Yidnekachew Melaku , Gebre Meseret , Negash Abel Abera
Published: November 2022

Background

Staphylococcus aureusandStreptococcus pneumoniaeare common inhabitants of the nasopharynx of children. HIV-infected children have higher risk of invasive diseases caused by these pathogens. With widespread use of pneumococcal conjugate vaccines and the emergence of methicillin-resistantS aureus, the interaction between S.aureusandS. pneumoniaeis of a particular significance. We sought to determine the magnitude of colonization by methicillin-sensitive and -resistant S.aureusand colonization byS. pneumoniae; associated risk factors and antimicrobial susceptibility pattern among HIV-Infected children in Addis Ababa, Ethiopia.

Method

A prospective observational study was conducted in 183 HIV-infected children at ALERT hospital Addis Ababa, Ethiopia from September 2016 to August 2018. S.aureusandS. pneumoniaewere identified using standard bacteriological techniques, antimicrobial susceptibility testing was performed on S.aureusand screening for methicillin resistance was carried out by amplifying themecAgene. Risk factors were analyzed by using binary logistic regression.

Results

The prevalence of nasopharyngealS. aureus, MRSA andS. pneumoniaecolonization were 27.3%, 2.7% and 43.2% respectively. Multivariable analysis indicated an inverse association betweenS. aureusand S.pneumoniaenasopharyngeal colonization (aOR, 0.49; CI, (0.24, 0.99);p= 0.046). The highest level of resistance in both methicillin sensitiveS. aureus(MSSA) and MRSA was observed against tetracycline.

Conclusions

We found an inverse association betweenS. aureusandS. pneumoniaecolonization among HIV-infected children. Continued assessment of the impact of pneumococcal conjugate vaccines and anti-retroviral therapy on nasopharyngeal bacterial ecology is warranted.
Ensuring learner-centred pedagogy in an open and distance learning environment by applying scaffolding and positive reinforcement
Authors: Ahmed Md. Meraz , Rahman Anika , Hossain Md. Kamal , Tambi Fatimah Binti
Published: November 2022

Purpose

This study was intended to ensure learner-centred pedagogy in an open and distance learning environment by applying scaffolding and positive reinforcement techniques.

Design/methodology/approach

This study critically analysed the context and current instructional practice of Bangladesh Open University (BOU) via document analysis and literature review. The conceptual framework of this study was adapted from the ADDIE model, i.e. the analysis, design, development, implementation and evaluation model.

Findings

The study explored that the instructional practice of BOU was dominated by teacher-centred pedagogy. Hence, to ensure learner-centred pedagogy, the researchers developed three model lesson plans. These lesson plans infused the theoretical directives of scaffolding and positive reinforcement as well as several assessment tasks which can assess the learners’ lower-order and higher-order thinking skills. The researchers also presented possible challenges for the sound implementation of these model lesson plans and suggested pragmatic solutions accordingly.

Originality/value

This study recommended that the combined application of scaffolding and positive reinforcement would effectively ensure learner-centred pedagogy.