bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic and functional analysis of proteins related to embryonic development of decidua in patients with recurrent pregnancy loss†
Authors: Xiong Yi-Meng , Pan Hai-Tao , Ding Hai-Gang , He Yao , Zhang Juan , Zhang Feng , Yu Bin , Zhang Tao , Huang He-Feng
Published: July 2021

Recurrent pregnancy loss (RPL) is defined as the loss of two or more consecutive pregnancies before the 20 weeks of gestation. RPL affects about 1–2% of couples trying to conceive; however, the mechanisms leading to this complication are largely unknown. Our previous studies using comparative proteomics identified 314 differentially expressed proteins (DEPs) in the placental villous. In this study, we identified 5479 proteins from a total of 34 157 peptides in decidua of patients with early RPL (data are available via ProteomeXchange with identifier PXD023849). Further analysis identified 311 DEPs in the decidua tissue; and 159 proteins were highly expressed, whereas 152 proteins were lowly expressed. These 311 proteins were further analyzed by using Ingenuity Pathway Analysis. The results suggested that 50 DEPs played important roles in the embryonic development. Upstream analysis of these DEPs revealed that angiotensinogen was the most important upstream regulator. Furthermore, protein–protein interaction analysis of the embryonic development DEPs from the placental villous and decidua was performed in the STRING database. This study identified several proteins specifically associated with embryonic development in decidua of patients with early RPL. Therefore, these results provide new insights into potential biological mechanisms, which may ultimately inform RPL.
Heat stress induces oxidative stress and activates the KEAP1-NFE2L2-ARE pathway in bovine endometrial epithelial cells
Authors: Murata Hirona , Kunii Hiroki , Kusama Kazuya , Sakurai Toshihiro , Bai Hanako , Kawahara Manabu , Takahashi Masashi
Published: July 2021

Heat stress adversely affects the reproductive function in cows. Although a relationship between heat stress and oxidative stress has been suggested, it has not been sufficiently verified in bovine endometrial epithelial cells. Here, we investigated whether oxidative stress is induced by heat stress in bovine endometrial epithelial cells under high temperature. Luciferase reporter assays showed that the reporter activity of heat shock element and antioxidant responsive element was increased in endometrial epithelial cells cultured under high temperature compared to that in cells cultured under basal (thermoneutral) temperature. Also, nuclear factor, erythroid 2 like 2 (NFE2L2), a master regulator of cellular environmental stress response, stabilized and the expression levels of antioxidant enzyme genes increased under high temperature. Immunostaining confirmed the nuclear localization of NFE2L2 in endometrial epithelial cells cultured under high temperature. Quantitative polymerase chain reaction analysis showed that the expression levels of representative inflammatory cytokine genes, such as prostaglandin-endoperoxide synthase 2 (PTGS2) and interleukin 8, were significantly decreased in endometrial epithelial cells cultured under high temperature compared to those in cells cultured under basal temperature. Thus, our results suggest that heat stress induces oxidative stress, whereas NFE2L2 plays a protective role in bovine endometrial epithelial cells cultured under heat stress conditions.
Transcriptome and proteome dynamics of cervical remodeling in the mouse during pregnancy
Authors: Nallasamy Shanmugasundaram , Palacios Hector H , Setlem Rohit , Colon Caraballo Mariano , Li Kelvin , Cao Edward , Shankaran Mahalakshmi , Hellerstein Marc , Mahendroo Mala
Published: July 2021

During gestation, the female reproductive tract must maintain pregnancy while concurrently preparing for parturition. Here, we explore the transitions in gene expression and protein turnover (fractional synthesis rates [FSR]) by which the cervix implements a transition from rigid to compliant. Shifts in gene transcription to achieve immune tolerance and alter epithelial cell programs begin in early pregnancy. Subsequently, in mid-to-late pregnancy transcriptional programs emerge that promote structural reorganization of the extracellular matrix (ECM). Stable isotope labeling revealed a striking slowdown of overall FSRs across the proteome on gestation day 6 that reverses in mid-to-late pregnancy. An exception was soluble fibrillar collagens and proteins of collagen assembly, which exhibit high turnover in nonpregnant cervix compared with other tissues and FSRs that continue throughout pregnancy. This finding provides a mechanism to explain how cross-linked collagen is replaced by newly synthesized, less cross-linked collagens, which allows increased tissue compliance during parturition. The rapid transition requires a reservoir of newly synthesized, less cross-linked collagens, which is assured by the high FSR of soluble collagens in the cervix. These findings suggest a previously unrecognized form of “metabolic flexibility” for ECM in the cervix that underlies rapid transformation in compliance to allow parturition.
Blood biomarkers reflect the effects of obesity and inflammation on the human breast transcriptome
Authors: Cho Byuri Angela , Iyengar Neil M , Zhou Xi Kathy , Morrow Monica , Giri Dilip D , Verma Akanksha , Elemento Olivier , Pollak Michael , Dannenberg Andrew J
Published: July 2021

Obesity is a risk factor for the development of post-menopausal breast cancer. Breast white adipose tissue (WAT) inflammation, which is commonly found in women with excess body fat, is also associated with increased breast cancer risk. Both local and systemic effects are probably important for explaining the link between excess body fat, adipose inflammation and breast cancer. The first goal of this cross-sectional study of 196 women was to carry out transcriptome profiling to define the molecular changes that occur in the breast related to excess body fat and WAT inflammation. A second objective was to determine if commonly measured blood biomarkers of risk and prognosis reflect molecular changes in the breast. Breast WAT inflammation was assessed by immunohistochemistry. Bulk RNA-sequencing was carried out to assess gene expression in non-tumorous breast. Obesity and WAT inflammation were associated with a large number of differentially expressed genes and changes in multiple pathways linked to the development and progression of breast cancer. Altered pathways included inflammatory response, complement, KRAS signaling, tumor necrosis factor α signaling via NFkB, interleukin (IL)6-JAK-STAT3 signaling, epithelial mesenchymal transition, angiogenesis, interferon γ response and transforming growth factor (TGF)-β signaling. Increased expression of several drug targets such as aromatase, TGF-β1, IDO-1 and PD-1 were observed. Levels of various blood biomarkers including high sensitivity C-reactive protein, IL6, leptin, adiponectin, triglycerides, high-density lipoprotein cholesterol and insulin were altered and correlated with molecular changes in the breast. Collectively, this study helps to explain both the link between obesity and breast cancer and the utility of blood biomarkers for determining risk and prognosis.
Long noncoding RNA MALAT1 sponging miR-26a-5p to modulate Smad1 contributes to colorectal cancer progression by regulating autophagy
Authors: Zhou Jiamin , Wang Miao , Mao Anrong , Zhao Yiming , Wang Longrong , Xu Ye , Jia Hao , Wang Lu
Published: July 2021

Accumulating evidences have suggested that bone morphogenetic protein (BMP)-Smad have a functional role in regulating autophagy in the development of human colorectal cancer (CRC). However, the regulatory mechanisms controlling this process remain unclear. Here, we showed that Smad1, the key effector of BMP2-Smad signaling, induces autophagy by upregulating autophagy-related gene 5 (ATG5) expression, and Smad1 binds to the proximal promoter to induce its expression. Moreover, BMP2 induces autophagy in CRC. Overexpression of Smad1 promotes tumorigenesis and migration of CRC cells, and knockdown of ATG5 is able to rescue the Smad1-induced promotion of CRC proliferation and migration partially. Mechanistically, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) may act as a competing endogenous RNA by binding with miR-26a-5p competitively and thus modulating the de-repression of downstream target Smad1. Furthermore, clinical analysis results show that Smad1 is positively correlated with MALAT1 and negatively correlated with miR-26a-5p in CRC samples. In conclusion, our results demonstrated that Smad1 may serve as an oncogene in CRC through autophagy.
Foetoscopy-assisted balloon valvuloplasty in a human foetus with disadvantageous intrauterine position: a case report
Authors: Kohl Thomas , Akin Ibrahim , Frommberger Juliane , Riehle Nadja , Schranz Dietmar
Published: July 2021

Background

Some foetuses scheduled for balloon valvuloplasty present with unfavourable lies that render a successful procedure unlikely or impossible. In these situations, foetal posturing previously has been achieved by maternal laparotomy. As a less invasive means, we demonstrate the feasibility of a minimally invasive foetoscopic approach.

Case summary

Percutaneous ultrasound-guided foetal balloon valvuloplasty for severe aortic valve stenosis was attempted in a human foetus at 29 + 4 weeks of gestation under general maternofoetal anaesthesia. Unfortunately, prior to the procedure, the foetus had been observed on several occasions remaining in a dorsoanterior cephalic position. Therefore, the left ventricle could not be accessed by the conventional percutaneous ultrasound-guided approach. In order to achieve the desired foetal lie, foetoscopic assistance was employed: using a standardized foetoscopic setup, a foetoscope and two graspers, the foetus was rotated in dorsoposterior position. After this manoeuver, successful balloon valvuloplasty was achieved. Mother and foetus tolerated the procedure well and complications were not observed.

Discussion

Foetoscopy-assisted foetal posturing offers itself as an alternative to maternal laparotomy in foetuses presenting with a persisting disadvantageous position at the time of balloon valvuloplasty. Due to the increased risks of preterm rupture of membranes and earlier delivery posed by the foetoscopic approach, this technique may preferably be used in more mature foetuses when foetal posturing cannot be achieved by other means.
How Can We Investigate Ancient Greek Categories Without the Influence of Our Own? Exploring Kinship Terminology Using Word2Vec
Authors: List Nicholas
Published: July 2021

Recent advances in Natural Language Processing (NLP) continue to open up new lines of enquiry for lexicography, especially for research areas concerned with semantic categorisation. The aims of this paper fall into two parts. In the first half, the NLP tool Word2Vec is introduced and discussed with respect to unsupervised category formation for Koine Greek, using kinship terms as a demonstration of the model’s utility. The latter half of the paper employs a prototype theory framework to analyse the model’s distributional information in the construction of new dictionary entries for each kinship term. Such NLP-based research highlights the importance of encyclopaedic information for the construction of lexical entries; it also significantly improves upon earlier attempts at categorisation for Koine Greek (Louw and Nida 1988), which fall victim to using the L1 categories of the lexicographer in the construction of semantic domains for the ancient language.
Phase retrieval of complex-valued objects via a randomized Kaczmarz method
Authors: Zhang Teng , Feng Yu
Published: July 2021

This paper investigates the convergence of the randomized Kaczmarz algorithm for the problem of phase retrieval of complex-valued objects. Although this algorithm has been studied for the real-valued case in [ 28], its generalization to the complex-valued case is nontrivial and has been left as a conjecture. This paper applies a different approach by establishing the connection between the convergence of the algorithm and the convexity of an objective function. Based on the connection, it demonstrates that when the sensing vectors are sampled uniformly from a unit sphere in ${\mathcal{C}}^n$ and the number of sensing vectors $m$ satisfies $m>O(n\log n)$ as $n, m\rightarrow \infty $, then this algorithm with a good initialization achieves linear convergence to the solution with high probability. The method can be applied to other statistical models of sensing vectors as well. A similar convergence result is established for the unitary model, where the sensing vectors are from the columns of random orthogonal matrices.

2000 Math Subject Classification: 68W20, 68W27, 92D25.
Mapping the prevalence and socioeconomic predictors of low birth weight among Bangladeshi newborns: evidence from the 2019 Multiple Indicator Cluster Survey
Authors: Ahmed Md Sabbir
Published: July 2021

Background

Low birth weight (LBW) remains a global concern for childhood morbidity and mortality. This study examined the socioeconomic factors associated with LBW among Bangladeshi newborns and drew a district-level prevalence map.

Methods

Data were extracted from the 2019 Multiple Indicator Cluster Survey for Bangladesh. Multivariate logistic regression was used to identify the predictors of LBW.

Results

The prevalence of LBW among Bangladeshi newborns was found to be 14.5%. Overall, the Eastern and South-Eastern regions had a higher burden of LBW. Mothers’ educational status, mode of delivery, wealth index quintile of the household and area were identified as independent predictors of newborns’ LBW. Mothers who completed primary and secondary education grades had a 1.6- and 1.3-fold higher possibility of having an LBW baby compared with those who completed higher secondary or higher educational grades (adjusted OR=1.62 and 1.32, 95% CI 1.21 to 2.18 and 1.06 to 1.65, respectively). Children belonging to the poorest households and residing in urban areas had a 1.4-fold higher likelihood of being LBW (p<0.05).

Conclusions

This study indicates that LBW is still highly prevalent in Bangladesh. Immediate public health action is required in the highly prevalent regions identified in this study.
Efficacy of Acupuncture on Pain Mechanisms, Inflammatory Responses, and Wound Healing in the Acute Phase of Major Burns: An Experimental Study on Rats
Authors: Abali Ayse Ebru , Cabioglu Tugrul , Bayraktar Nilufer , Ozdemir Binnaz Handan , Moray Gokhan , Haberal Mehmet
Published: July 2021

We investigated acupuncture, a potential contributor for burn care, on physiological and pathological pain mechanisms and systemic and local inflammatory responses in a rat experimental burn model. Forty male Sprague–Dawley rats were divided into two groups. One-hour groups (five rats/group) were observed for 1 hour and included Sh1 (sham/observation), ShA1 (sham + acupuncture/observation), Brn1 (burn/observation), and BrnA1 (burn + acupuncture/observation). Seven-day groups (five rats/group) were observed for 7 days and included Sh7 (sham/observation), ShA7 (sham + acupuncture/observation), Brn7 (burn/observation), and BrnA7 (burn + acupuncture/observation). “Pain–distress scores” were noted daily, and acupuncture was repeated within every wound-dressing change on alternate days. After observation periods, blood samples for interleukin 6 and beta-endorphin and skin biopsies for inflammatory changes and immunohistochemical staining of interleukin 6 were collected for analysis(P < .05). In 1-hour groups, interleukin 6 accumulation in burn wounds of BrnA1 was less than Brn1, with Brn1 having the highest mean blood level (P < .05). Mean beta-endorphin levels were higher in ShA1, Brn1, and BrnA1 than in Sh1 (P < .05). In all 7-day groups, the agonizing period was 48 to 72 hours after burn, with Brn7 most affected (P < .05). Microvessels were multiplied in the Brn7 group, with significantly higher numbers in burn wounds of BrnA7 (P ˂ .05). Burn wounds of BrnA7 had less accumulation of interleukin 6 than Brn7 with the Brn7 group having the highest mean blood level and Sh7, ShA7, and BrnA7 having similarly low levels (P ˃ .05). Beta-endorphin levels in ShA7, Brn7, and BrnA7 were lower than in Sh7 (P < .05). Acupuncture contributed to the management of physiological and pathological pain, modulation of inflammatory responses, and associated enhancement of angiogenesis in the acute phase of burn injury in rats.
Risk Premia and Lévy Jumps: Theory and Evidence
Authors: Fallahgoul Hasan , Hugonnier Julien , Mancini Loriano
Published: July 2021

We develop a novel class of time-changed Lévy models, which are tractable and readily applicable, capture the leverage effect, and exhibit pure jump processes with finite or infinite activity. Our models feature four nested processes reflecting market, volatility and jump risks, and observation error of time changes. To operationalize the models, we use volume-based proxies of the unobservable time changes. To estimate risk premia, we derive the change of measure analytically. An extensive time series and option pricing analysis of sixteen time-changed Lévy models shows that infinite activity processes carry significant jump risk premia, and largely outperform many finite activity processes.
Abdominal wall endometrioma presenting as a cystic abdominal wall mass: a case report and literature review
Authors: Davis Tyler , Moudy Paige , Barghuthi Lutfi , Abdelgawad Mohamed , Ismael Hishaam
Published: July 2021

Endometriosis is classically defined as ‘the presence of endometrial glands and stroma outside of the uterine cavity and musculature’. Although it most commonly occurs in the pelvis, various extrapelvic locations have been reported in the literature. There seems to be a strong association between abdominal wall endometriomas and previous surgical scars. In female patients presenting with a cyclically painful abdominal wall mass, a high index of suspicion for endometrioma must be maintained, especially in the setting of previous gynecologic surgery. Although there may be a role for medical management of symptoms, the most definitive treatment of an abdominal wall endometrioma appears to be wide local excision with negative margins. This paper presents a 39-year-old female with an extensive gynecologic surgical history presenting with a 6 × 6 cm cyclically tender abdominal wall endometrioma treated with wide local excision.
Macular Findings of Patients on Pentosan Polysulfate Sodium
Authors: Blackorby Barton L , Banda Himanshu , Smith Bradley T , Shah Gaurav K
Published: July 2021

Introduction

In 2018, a unique maculopathy associated with chronic pentosan polysulfate sodium (PPS) use for the treatment of interstitial cystitis (IC) was described, where the authors detailed macular retinal pigment epithelial abnormalities in six patients. In this paper, a retrospective study of a larger patient pool at one large tertiary retina practice was undertaken to evaluate patients taking PPS and their macular findings.

Materials and methods

A retrospective chart review was performed on all patients presenting to a single large retina practice between 2011 and 2019. Patient’s macular diagnosis, findings, optical coherence tomography scans, and macular auto-fluorescent scans were assessed. This project was Institutional Review Board (IRB) approved by the St Luke’s Hospital IRB board (St Louis, MO, USA).

Results

Fifty-five patients were identified as taking PPS for IC. Fifty-three patients were found to have a diagnosis consistent with changes attributable to known macular diseases to include macular degeneration and pattern dystrophies. Two (4%) of fifty-five patients had macular findings suggestive of PPS toxicity. The first was a 58-year-old female with subtle retinal pigment epithelium (RPE) deposits on optical coherence tomography that exhibited hyper-autofluorescence. The second was a 72-year-old female with 14 years of PPS use who exhibited RPE excrescences and parafoveal areas of atrophy.

Conclusions

Pentosan polysulfate sodium may be the cause of macular findings in a small percentage of patients referred to a tertiary retina practice. Although causation of macular changes with PPS use has yet to be elucidated, clinicians should be aware of this possibility when assessing patients with atypical macular findings. Future longitudinal studies are necessary to evaluate a definitive relationship. This paper should remind all clinicians of the importance of a throughout review of the patient’s medication list as novel toxicities may become apparent years after initial FDA trials. The strength of this study is the larger patient population compared to earlier studies, and the main weaknesses include the retrospective nature of the study, lack of family and genetic testing, and lack of multimodal imaging for all patients.
Defective Satellite DNA Clustering into Chromocenters Underlies Hybrid Incompatibility in Drosophila
Authors: Jagannathan Madhav , Yamashita Yukiko M
Published: July 2021

Although rapid evolution of pericentromeric satellite DNA repeats is theorized to promote hybrid incompatibility (HI) (Yunis and Yasmineh 1971; Henikoff et al. 2001; Ferree and Barbash 2009; Sawamura 2012; Jagannathan and Yamashita 2017), how divergent repeats affect hybrid cells remains poorly understood. Recently, we demonstrated that sequence-specific DNA-binding proteins cluster satellite DNA from multiple chromosomes into “chromocenters,” thereby bundling chromosomes to maintain the entire genome in a single nucleus (Jagannathan et al. 2018, 2019). Here, we show that ineffective clustering of divergent satellite DNA in the cells of Drosophila hybrids results in chromocenter disruption, associated micronuclei formation, and tissue atrophy. We further demonstrate that previously identified HI factors trigger chromocenter disruption and micronuclei in hybrids, linking their function to a conserved cellular process. Together, we propose a unifying framework that explains how the widely observed satellite DNA divergence between closely related species can cause reproductive isolation.
Integrated stress response control of granulosa cell translation and proliferation during normal ovarian follicle development
Authors: Cari Evelyn Llerena , Hagen-Lillevik Synneva , Giornazi Asma , Post Miriam , Komar Anton A , Appiah Leslie , Bitler Benjamin , Polotsky Alex J , Santoro Nanette , Kieft Jeffrey , Lai Kent , Johnson Joshua
Published: July 2021

Mechanisms that directly control mammalian ovarian primordial follicle (PF) growth activation and the selection of individual follicles for survival are largely unknown. Follicle cells produce factors that can act as potent inducers of cellular stress during normal function. Consistent with this, we show here that normal, untreated ovarian cells, including pre-granulosa cells of dormant PFs, express phenotype and protein markers of the activated integrated stress response (ISR), including stress-specific protein translation (phospho-Serine 51 eukaryotic initiation factor 2 α ; P-EIF2 α ), active DNA damage checkpoints, and cell cycle arrest. We further demonstrate that mRNAs upregulated in primary (growing) follicles versus arrested PFs mostly include stress-responsive upstream open reading frames (uORFs). Treatment of a granulosa cell (GC) line with the PF growth trigger tumor necrosis factor alpha results in the upregulation of a ‘stress-dependent’ translation profile. This includes further elevated P-eIF2 α and a shift of uORF-containing mRNAs to polysomes. Because the active ISR corresponds to slow follicle growth and PF arrest, we propose that repair and abrogation of ISR checkpoints (e.g. checkpoint recovery) drives the GC cell cycle and PF growth activation (PFGA). If cellular stress is elevated beyond a threshold(s) or, if damage occurs that cannot be repaired, cell and follicle death ensue, consistent with physiological atresia. These data suggest an intrinsic quality control mechanism for immature and growing follicles, where PFGA and subsequent follicle growth and survival depend causally upon ISR resolution, including DNA repair and thus the proof of genomic integrity.
A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase
Authors: Xu Xinzhou , Zhang Lu , Chu Julie Tung Sem , Wang Yuqing , Chin Alex Wing Hong , Chong Tin Hang , Dai Zixi , Poon Leo Lit Man , Cheung Peter Pak-Hang , Huang Xuhui
Published: July 2021

During RNA elongation, the influenza A viral (IAV) RNA-dependent RNA polymerase (RdRp) residues in the active site interact with the triphosphate moiety of nucleoside triphosphate (NTP) for catalysis. The molecular mechanisms by which they control the rate and fidelity of NTP incorporation remain elusive. Here, we demonstrated through enzymology, virology and computational approaches that the R239 and K235 in the PB1 subunit of RdRp are critical to controlling the activity and fidelity of transcription. Contrary to common beliefs that high-fidelity RdRp variants exert a slower incorporation rate, we discovered a first-of-its-kind, single lysine-to-arginine mutation on K235 exhibited enhanced fidelity and activity compared with wild-type. In particular, we employed a single-turnover NTP incorporation assay for the first time on IAV RdRp to show that K235R mutant RdRp possessed a 1.9-fold increase in the transcription activity of the cognate NTP and a 4.6-fold increase in fidelity compared to wild-type. Our all-atom molecular dynamics simulations further elucidated that the higher activity is attributed to the shorter distance between K235R and the triphosphate moiety of NTP compared with wild-type. These results provide novel insights into NTP incorporation and fidelity control mechanisms, which lay the foundation for the rational design of IAV vaccine and antiviral targets.
The lane-switch mechanism for nucleosome repositioning by DNA translocase
Authors: Nagae Fritz , Brandani Giovanni B , Takada Shoji , Terakawa Tsuyoshi
Published: July 2021

Translocases such as DNA/RNA polymerases, replicative helicases, and exonucleases are involved in eukaryotic DNA transcription, replication, and repair. Since eukaryotic genomic DNA wraps around histone octamers and forms nucleosomes, translocases inevitably encounter nucleosomes. A previous study has shown that a nucleosome repositions downstream when a translocase collides with the nucleosome. However, the molecular mechanism of the downstream repositioning remains unclear. In this study, we identified the lane-switch mechanism for downstream repositioning with molecular dynamics simulations and validated it with restriction enzyme digestion assays and deep sequencing assays. In this mechanism, after a translocase unwraps nucleosomal DNA up to the site proximal to the dyad, the remaining wrapped DNA switches its binding lane to that vacated by the unwrapping, and the downstream DNA rewraps, completing downstream repositioning. This mechanism may have broad implications for transcription through nucleosomes, histone recycling, and nucleosome remodeling.
NMPylation and de-NMPylation of SARS-CoV-2 nsp9 by the NiRAN domain
Authors: Wang Bing , Svetlov Dmitri , Artsimovitch Irina
Published: July 2021

The catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) contains two active sites that catalyze nucleotidyl-monophosphate transfer (NMPylation). Mechanistic studies and drug discovery have focused on RNA synthesis by the highly conserved RdRp. The second active site, which resides in a Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain, is poorly characterized, but both catalytic reactions are essential for viral replication. One study showed that NiRAN transfers NMP to the first residue of RNA-binding protein nsp9; another reported a structure of nsp9 containing two additional N-terminal residues bound to the NiRAN active site but observed NMP transfer to RNA instead. We show that SARS-CoV-2 RdRp NMPylates the native but not the extended nsp9. Substitutions of the invariant NiRAN residues abolish NMPylation, whereas substitution of a catalytic RdRp Asp residue does not. NMPylation can utilize diverse nucleotide triphosphates, including remdesivir triphosphate, is reversible in the presence of pyrophosphate, and is inhibited by nucleotide analogs and bisphosphonates, suggesting a path for rational design of NiRAN inhibitors. We reconcile these and existing findings using a new model in which nsp9 remodels both active sites to alternately support initiation of RNA synthesis by RdRp or subsequent capping of the product RNA by the NiRAN domain.
The Initial Step Towards Establishing a Quantitative, Magnetic Resonance Imaging-Based Framework for Response Assessment of Spinal Metastases After Stereotactic Body Radiation Therapy
Authors: Jabehdar Maralani Pejman , Tseng Chia-Lin , Baharjoo Hamidreza , Wong Erin , Kapadia Anish , Dasgupta Archya , Howard Peter , Chan Aimee K M , Atenafu Eshetu G , Lu Hua , Tyrrell Pascal , Das Sunit , Payabvash Seyedmehdi , Detsky Jay , Husain Zain , Myrehaug Sten , Soliman Hany , Chen Hanbo , Heyn Chris , Symons Sean , Sahgal Arjun
Published: July 2021

BACKGROUND

There are no established threshold values regarding the degree of growth on imaging when assessing response of spinal metastases treated with stereotactic body radiation therapy (SBRT).

OBJECTIVE

To determine a magnetic resonance imaging-based minimum detectable difference (MDD) in gross tumor volume (GTV) and its association with 1-yr radiation site-specific (RSS) progression-free survival (PFS).

METHODS

GTVs at baseline and first 2 post-SBRT scans (Post1 and Post2, respectively) for 142 spinal segments were contoured, and percentage volume change between scans calculated. One-year RSS PFS was acquired from medical records. The MDD was determined. The MDD was compared against optimal thresholds of GTV changes associated with 1-yr RSS PFS using Youden's J index, and receiver operating characteristic curves between timepoints compared to determine which timeframe had the best association.

RESULTS

A total of 17 of the 142 segments demonstrated progression. The MDD was 10.9%. Baseline-Post2 demonstrated the best performance (area under the curve [AUC] 0.90). Only Baseline-Post2 had an optimal threshold > MDD at 14.7%. Due to large distribution of GTVs, volumes were split into tertiles. Small tumors (GTV < 2 cc) had optimal thresholds of 42.0%, 71.3%, and 37.2% at Baseline-Post1 (AUC 0.81), Baseline-Post2 (AUC 0.89), and Post1-Post2 (AUC 0.77), respectively. Medium tumors (2 ≤ GTV ≤ 8.3 cc) all demonstrated optimal thresholds < MDD, with AUCs ranging from 0.65 to 0.84. Large tumors (GTV > 8.3 cc) had 2 timepoints where optimal thresholds > MDD: Baseline-Post2 (13.3%; AUC 0.97) and Post1-Post2 (11.8%; AUC 0.66). Baseline-Post2 had the best association with RSS PFS for all tertiles.

CONCLUSION

Given a MDD of 10.9%, for small GTVs, larger (>37%) changes were required before local failure could be determined, compared to 11% to 13% for medium/large tumors.
Incidence, Duration, and Risk Factors Associated With Missed Opportunities to Diagnose Herpes Simplex Encephalitis: A Population-Based Longitudinal Study
Authors: Miller Aaron C , Koeneman Scott H , Arakkal Alan T , Cavanaugh Joseph E , Polgreen Philip M
Published: July 2021

Background

Delays in diagnosing herpes simplex encephalitis (HSE) are associated with increased morbidity and mortality. The purpose of this paper is to determine the frequency and duration of diagnostic delays for HSE and risk factors for diagnostic delays.

Methods

Using data from the IBM Marketscan Databases, 2001–2017, we performed a retrospective cohort study of patients with HSE. We estimated the number of visits with HSE-related symptoms before diagnosis that would be expected to occur in the absence of delays and compared this estimate to the observed pattern of visits. Next, we used a simulation-based approach to compute the number of visits representing a delay, the number of missed diagnostic opportunities per case patient, and the duration of delays. We also investigated potential risk factors for delays.

Results

We identified 2667 patients diagnosed with HSE. We estimated 45.9% (95% confidence interval [CI], 43.6%–48.1%) of patients experienced at least 1 missed opportunity; 21.9% (95% CI, 17.3%–26.3%) of these patients had delays lasting >7 days. Risk factors for delays included being seen only in the emergency department, age <65, or a history of sinusitis or schizophrenia.

Conclusions

Many patients with HSE experience multiple missed diagnostic opportunities before diagnosis.
GLABRA2-based selection efficiently enriches Cas9-generated nonchimeric mutants in the T1 generation
Authors: Kong Xiangjiu , Pan Wenbo , Sun Nengxu , Zhang Tingyu , Liu Lijing , Zhang Huawei
Published: July 2021

The CRISPR/Cas9 system is a widely used tool for genome editing in plants. In Arabidopsis (Arabidopsis thaliana), egg cell-specific promoters driving Cas9 expression have been applied to reduce the proportion of T1 transformants that are chimeras; however, this approach generally leads to relatively low mutagenesis rates. In this study, a GLABRA2 mutation-based visible selection (GBVS) system was established to enrich nonchimeric mutants among T1 plants generated by an egg cell-specific CRISPR/Cas9 system. GBVS generally enhanced mutation screening, increasing the frequency by 2.58- to 7.50-fold, and 25%–48.15% of T1 plants selected through the GBVS system were homozygous or biallelic mutants, which was 1.71- to 7.86-fold higher than the percentage selected using the original system. The mutant phenotypes of T2 plants were not obviously affected by the glabrous background for all four target genes used in this study. Additionally, the nonchimeric pyrabactin resistance 1 (PYR1)/PYR1-like 1 (PYL1) and PYL2 triple mutant pyr1/pyl1/pyl2 could be obtained in the T1 generation with a ratio of 26.67% when GBVS was applied. Collectively, our results show that compared with the known CRISPR/Cas9 systems, the GBVS system described here saves more time and labor when used for the obtainment of homozygous or biallelic monogenic mutants and nonchimeric polygenic mutants in Arabidopsis.
Costs of Guillain-Barré Syndrome in the Brazilian Federal District: the patients’ perspective
Authors: Oliveira Ana Flávia de Morais , Gallo Luciana Gerra , Bastos Mábia Milhomem , Abrahão Amanda Amaral , Garcia Klauss Kleydmann Sabino , de Carvalho Jeane Kelly Silva , Macedo Lilian de Paula , de Araújo Wildo Navegantes , Peixoto Henry Maia
Published: July 2021

Background

Although rare, Guillain-Barré Syndrome (GBS) has a high economic burden, with consequences for families and society. This study aimed to estimate the total cost of GBS, per individual and per variant of the disease, as well as its effect on household income, from the perspective of patients.

Methods

This was a cost-of-illness study from the perspective of patients and their families, with a time horizon from disease onset to 6 mo after discharge. The total cost of GBS was estimated by bottom-up microcosting, considering direct and indirect costs.

Results

The median cost of GBS per individual was US$1635.5, with direct costs accounting for 64.3% of this amount. Among the variants analyzed, acute motor sensory axonal neuropathy (US$4660.1) and acute inflammatory demyelinating polyneuropathy (US$2017.0) exhibited the highest costs compared with acute motor axonal neuropathy (US$1635.5) and Miller Fisher Syndrome (US$1464.8). The costs involved compromise more than 20% of the household income of 22 (47.8%) patients.

Conclusions

This study demonstrated how costly GBS can be. It is hoped that decision-makers will analyze these results with a view to improving the structure of healthcare services.
Cryptosporidiosis is predominantly an urban, anthroponotic infectious disease among Zambian children
Authors: Banda Barbara , Siwila Joyce , Mukubesa Andrew N , Chitanga Simbarashe , Kaonga Patrick , Changula Katendi , Simulundu Edgar , Saasa Ngonda , Kelly Paul
Published: July 2021

Background

Cryptosporidium species are leading causes of diarrhoea in children and immunocompromised individuals. This study aimed to characterise Cryptosporidium species from children in rural and urban settings of Zambia.

Methods

Stool samples collected from 490 children aged <5 y with diarrhoea were assessed for Cryptosporidium oocysts microscopically. A structured questionnaire was used to collect demographic and socioeconomic characteristics. Positive samples were subjected to PCR and gp60 sequence analysis.

Results

The overall prevalence was 10% (50/490, 95% CI 7.8 to 13.2) with a peak in March, the late rainy season. Children who came from households where boiling water was not practised (OR=2.5, 95% CI 1.29 to 5.17; p=0.007) or who had experienced recurrent episodes of diarrhoea (OR=9.31, 95% CI 3.02 to 28.73; p=0.001) were more likely to have Cryptosporidium infection. Genotyping of 16 positive samples (14 from urban and 2 from rural sources) revealed Cryptosporidium hominis (14/16) and Cryptosporidium parvum (2/16). The Cryptosporidium hominis subtypes identified were Ia, Ib and Ie with subtype families IeAIIG3 (1), IbA9G3R2 (2), IaA31R3 (3), IbA9G3 (5), IaA27R3 (1), IaA30R3 (1) and Ia (1). Subtypes IbA9G3 and Ia were identified in children from a rural area. Cryptosporidium parvum subtypes were IIcA5G3R2 (1) and IIcA5G3a (1).

Conclusions

All isolates successfully genotyped were C. hominis or anthroponotic C. parvum, suggesting that anthroponotic transmission dominates in Lusaka and the surrounding countryside.
An Examination of Apple Powdery Mildew and the Biology of Podosphaera leucotricha from Past to Present
Authors: Strickland David A. , Hodge Kathie T. , Cox Kerik D.
Published: July 2021

Within is a comprehensive review of current apple powdery mildew literature, with the taxonomy, morphology, and life cycle of the causal phytopathogen Podosphaera leucotricha described. A discussion of economic impact, environmental aspects contributing to apple powdery mildew epidemiology, options for cultural, chemical, and biopesticide disease control, and fungicide resistance in P. leucotricha is also detailed. The present status of breeding for host resistance and apple cultivar susceptibility is discussed. Finally, emerging research into the biology and management of apple powdery mildew is discussed along with how they may aid future research endeavors.
Development of a Real-Time Loop-Mediated Isothermal Amplification Assay for Stromatinia cepivora in Response to an Outbreak in Northern Idaho
Authors: Woodhall James , Harrington Miranda , Brown Lara , Jensen Jennifer , Painter Kate
Published: July 2021

Stromatinia cepivora is the causal agent of white rot disease of Allium species. In 2018, white rot was observed in Boundary County in Northern Idaho in garlic and onion plants in a variety of home and market garden operations. Because the university diagnostic laboratory for Idaho is situated in Parma within a regulated area for S. cepivora, a point-of-care (POC) assay using real-time loop-mediated isothermal amplification (LAMP) was developed to minimize the amount of material potentially sent to the diagnostic laboratory. The LAMP assay was used with a BioRanger platform, and although the limit of detection meant it was 100 times less sensitive than TaqMan, it was capable of detecting a single sclerotium. This study demonstrates the rapid development and deployment of a POC-suitable LAMP assay. Despite limitations in sensitivity and dynamic range compared with real-time PCR, POC LAMP assays are advantageous where biosecurity concerns prohibit the movement of material suitable for diagnosis as well as facilitating engagement with growers.
Perioperative management considerations in patients taking prescribed psychoactive medications (including those for depression and Parkinson's disease)
Authors: Ho Serene , Wong Adrian
Published: July 2021

Purpose of review

Given the number of drugs available in the anaesthetist's armamentarium, drug interactions need to be managed. This is particularly true of psychoactive medications which primarily act on the central nervous system, targeting neurotransmitter pathways often affected by anaesthetic agents. This review gives an overview of the potential interactions of commonly used psychoactive medications with anaesthetic agents and hence their perioperative considerations. As anaesthetists will already be very familiar with the benzodiazepines, they will not be discussed here. Electroconvulsive therapy will also not be discussed.

Recent findings

A wide range of psychoactive medications can interact with drugs commonly used in perioperative care including anaesthetic agents. There is limited clinical research into their effects and hence these interactions are based on known pharmacological actions.

A cautious, pragmatic approach is recommended when managing patients on psychoactive medications requiring anaesthesia as part of their medical care.
Geographic variations in the incidence of congenital hypothyroidism in China: a retrospective study based on 92 million newborns screened in 2013–2018
Authors: Yao Yong-Na , Yuan Xue-Lian , Zhu Jun , Xiang Liang-Cheng , Li Qi , Deng Kui , Li Xiao-Hong , Liu Han-Min
Published: July 2021

Background:

Although congenital hypothyroidism (CH) has been widely studied in Western countries, CH incidence at different administrative levels in China during the past decade remains unknown. This study aimed to update the incidence and revealed the spatial pattern of CH incidence in the mainland of China, which could be helpful in the planning and implementation of preventative measures.

Methods:

The data used in our study were derived from 245 newborns screening centers that cover 30 provinces of the Chinese Newborn Screening Information System. Spatial auto-correlation was analyzed by Global Moran I and Getis-Ord Gi statistics at the provincial level. Kriging interpolation methods were applied to estimate a further detailed spatial distribution of CH incidence at city level throughout the mainland of China, and Kulldorff space scanning statistical methods were used to identify the spatial clusters of CH cases at the city level.

Results:

A total of 91,921,334 neonates were screened from 2013 to 2018 and 42,861 cases of primary CH were identified, yielding an incidence of 4.66 per 10,000 newborns screened (95% confidence interval [CI]: 4.62–4.71). Neonates in central (risk ratio [RR] = 0.84, 95% CI: 0.82–0.85) and western districts (RR = 0.71, 95% CI: 0.69–0.73) had lower probability of CH cases compared with the eastern region. The CH incidence indicated a moderate positive global spatial autocorrelation (Global Moran I value = 0.394, P 
< 0.05), and the CH cases were significantly clustered in spatial distribution. A most likely city-cluster (log-likelihood ratio [LLR] = 588.82, RR = 2.36, P 
< 0.01) and 25 secondary city-clusters of high incidence were scanned. The incidence of each province and each city in the mainland of China was estimated by kriging interpolation, revealing the most affected province and city to be Zhejiang Province and Hangzhou city, respectively.

Conclusion:

This study offers an insight into the space clustering of CH incidence at provincial and city scales. Future work on environmental factors need to focus on the effects of CH occurrence.
Prescription Opioid Laws and Opioid Dispensing in US Counties
Authors: Martins Silvia S. , Bruzelius Emilie , Stingone Jeanette A. , Wheeler-Martin Katherine , Akbarnejad Hanane , Mauro Christine M. , Marziali Megan E. , Samples Hillary , Crystal Stephen , Davis Corey S. , Rudolph Kara E. , Keyes Katherine M. , Hasin Deborah S. , Cerdá Magdalena
Published: July 2021

Background:

Hundreds of laws aimed at reducing inappropriate prescription opioid dispensing have been implemented in the United States, yet heterogeneity in provisions and their simultaneous implementation have complicated evaluation of impacts. We apply a hypothesis-generating, multistage, machine-learning approach to identify salient law provisions and combinations associated with dispensing rates to test in future research.

Methods:

Using 162 prescription opioid law provisions capturing prescription drug monitoring program (PDMP) access, reporting and administration features, pain management clinic provisions, and prescription opioid limits, we used regularization approaches and random forest models to identify laws most predictive of county-level and high-dose dispensing. We stratified analyses by overdose epidemic phases—the prescription opioid phase (2006–2009), heroin phase (2010–2012), and fentanyl phase (2013–2016)—to further explore pattern shifts over time.

Results:

PDMP patient data access provisions most consistently predicted high-dispensing and high-dose dispensing counties. Pain management clinic-related provisions did not generally predict dispensing measures in the prescription opioid phase but became more discriminant of high dispensing and high-dose dispensing counties over time, especially in the fentanyl period. Predictive performance across models was poor, suggesting prescription opioid laws alone do not strongly predict dispensing.

Conclusions:

Our systematic analysis of 162 law provisions identified patient data access and several pain management clinic provisions as predictive of county prescription opioid dispensing patterns. Future research employing other types of study designs is needed to test these provisions’ causal relationships with inappropriate dispensing and to examine potential interactions between PDMP access and pain management clinic provisions. See video abstract at, http://links.lww.com/EDE/B861.
Swabs Containing Tea Tree Oil and Chamomile Oil Versus Baby Shampoo in Patients With Seborrheic Blepharitis: A Double-Blind Randomized Clinical Trial
Authors: Mergen Burak , Arici Ceyhun , Yildiz-Tas Ayse , Bahar-Tokman Hrisi , Tokuc Edip , Ozturk-Bakar Yesim , Kutlubay Zekayi , Sahin Afsun
Published: July 2021

Purpose:

The comparison of the efficacy of swabs containing tea tree oil and chamomile oil and baby shampoo (BS) in the treatment of seborrheic blepharitis was aimed.

Methods:

This randomized, double-blind, parallel-group, active control, multicenter clinical trial included patients with seborrheic blepharitis using block randomization (BS, n=23; swabs, n=26). Patients were treated with BS or swabs for 8 weeks followed by 4 weeks of treatment withdrawal. Change in Blepharitis Symptom measure (BLISS), Demodex count, Ocular Surface Disease Index (OSDI) score, Schirmer test, tear breakup time (TBUT), noninvasive TBUT (NI-TBUT), corneal staining, and meibography at different visits (baseline, fourth, , and 12th week) were the main outcome measures.

Results:

Patients in both groups showed similar baseline parameters (P>0.05). Patients using swabs showed significantly lower BLISS scores compared with patients using BS at the 4th, 8th, and 12th week visits (3.6±6.1 vs. 6.3±4.5 P=0.011; 1.1±2.8 vs. 6.6±6.7, P<0.001; 0.9±2.8 vs. 5.7±6.6, P=0.002, respectively). Patients using swabs showed improvement in OSDI scores after 8 weeks of treatment compared with the baseline visit (P<0.001). Despite a similar Demodex reduction effect in both treatment arms even after 4 weeks of treatment (P<0.001), both treatment modalities did not show any effect on the other parameters.

Conclusion:

Although both swabs and BS showed efficacy for the treatment of seborrheic blepharitis in terms of the Demodex reduction and symptomatic improvement, swabs may provide better symptomatic improvement. Four weeks of treatment discontinuation may not cause any recurrence in the symptoms or Demodex infestation.