bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-Free Fetal DNA for Genetic Evaluation in Copenhagen Pregnancy Loss Study (COPL): A Prospective Cohort Study
Authors: Schlaikjær Hartwig Tanja , Ambye Louise , Gruhn Jennifer R. , Petersen Jesper Friis , Wrønding Tine , Amato Letizia , Chi-Ho Chan Andrew , Ji Boyang , Bro-Jørgensen Maiken Hemme , Werge Lene , Petersen Mette Marie Babiel Schmidt , Brinkmann Clara , Petersen Julie Birch , Dunø Morten , Bache Iben , Herrgård Markus J. , Jørgensen Finn Stener , Hoffmann Eva R. , Nielsen Henriette Svarre ,   and The COPL Consortium
Published: June 2023

(Abstracted from Lancet 2023;401:762–771
Spontaneous pregnancy loss occurs in approximately 1 in 4 pregnancies; however, diagnostic workup is mostly restricted to women with recurrent pregnancy loss. The lack of workup on first pregnancy loss is likely a result of the high de novo fetal aneuploidy rate; however, this ignores the association of euploid pregnancy loss with an increased risk of future losses.
Modern antiretroviral regimens in pregnant women: virologic outcomes and durability
Authors: Smith Christiana , Silveira Lori , Crotteau Megan , Garth Krystle , Canniff Jennifer , Fetters Kirk B. , Lazarus Sarah , Capraro Shannon , Weinberg Adriana 
Published: June 2023

Objectives:
Data are lacking on the virologic efficacy and durability of modern antiretroviral treatment (ART) regimens during pregnancy. We compared virologic outcomes at delivery among women receiving dolutegravir versus other ART and the rate of change of the initial pregnancy regimen.

Design:
Single site retrospective cohort between 2009-2019.

Methods:
We used univariable and multivariable generalized estimating equations to model the relationship between the maternal ART anchor and the proportion of women with a viral load ≥20 HIV RNA copies/mL of plasma closest to delivery (suboptimal virologic control) and with a viral load ≥20 copies/mL at any time in the third trimester. We also compared changes in ART during pregnancy.

Results:
We evaluated 230 pregnancies in 173 mothers. Rates of optimal virologic control at delivery did not significantly differ in mothers who received dolutegravir (93.1%), rilpivirine (92.1%), boosted darunavir (82.6%), or efavirenz (76.9%), but were significantly lower among mothers receiving atazanavir (49.0%) or lopinavir (40.9%). The odds of having a viral load ≥20 copies/mL at any time in the third trimester was also higher for atazanavir and lopinavir. Raltegravir, elvitegravir, or bictegravir were used in <10 mothers at delivery, which precluded statistical analyses. The frequency of change in ART was significantly higher in mothers who initially received elvitegravir (68%) or efavirenz (47%) than dolutegravir (18%).

Conclusions:
Dolutegravir-, rilpivirine- and boosted darunavir-containing regimens conferred excellent virologic control in pregnancy. Atazanavir and lopinavir, elvitegravir, and efavirenz were associated with either high rates of virologic failure or regimen change during pregnancy.
Automatic Detection of Pancreatic Lesions and Main Pancreatic Duct Dilatation on Portal Venous CT Scans Using Deep Learning
Authors: Abi Nader Clément , Vetil Rebeca , Wood Laura Kate , Rohe Marc-Michel , Bône Alexandre , Karteszi Hedvig , Vullierme Marie-Pierre 
Published: June 2023

Objectives
This study proposes and evaluates a deep learning method to detect pancreatic neoplasms and to identify main pancreatic duct (MPD) dilatation on portal venous computed tomography scans.

Materials and Methods
A total of 2890 portal venous computed tomography scans from 9 institutions were acquired, among which 2185 had a pancreatic neoplasm and 705 were healthy controls. Each scan was reviewed by one in a group of 9 radiologists. Physicians contoured the pancreas, pancreatic lesions if present, and the MPD if visible. They also assessed tumor type and MPD dilatation. Data were split into a training and independent testing set of 2134 and 756 cases, respectively.
A method to detect pancreatic lesions and MPD dilatation was built in 3 steps. First, a segmentation network was trained in a 5-fold cross-validation manner. Second, outputs of this network were postprocessed to extract imaging features: a normalized lesion risk, the predicted lesion diameter, and the MPD diameter in the head, body, and tail of the pancreas. Third, 2 logistic regression models were calibrated to predict lesion presence and MPD dilatation, respectively. Performance was assessed on the independent test cohort using receiver operating characteristic analysis. The method was also evaluated on subgroups defined based on lesion types and characteristics.

Results
The area under the curve of the model detecting lesion presence in a patient was 0.98 (95% confidence interval [CI], 0.97–0.99). A sensitivity of 0.94 (469 of 493; 95% CI, 0.92–0.97) was reported. Similar values were obtained in patients with small (less than 2 cm) and isodense lesions with a sensitivity of 0.94 (115 of 123; 95% CI, 0.87–0.98) and 0.95 (53 of 56, 95% CI, 0.87–1.0), respectively. The model sensitivity was also comparable across lesion types with values of 0.94 (95% CI, 0.91–0.97), 1.0 (95% CI, 0.98–1.0), 0.96 (95% CI, 0.97–1.0) for pancreatic ductal adenocarcinoma, neuroendocrine tumor, and intraductal papillary neoplasm, respectively. Regarding MPD dilatation detection, the model had an area under the curve of 0.97 (95% CI, 0.96–0.98).

Conclusions
The proposed approach showed high quantitative performance to identify patients with pancreatic neoplasms and to detect MPD dilatation on an independent test cohort. Performance was robust across subgroups of patients with different lesion characteristics and types. Results confirmed the interest to combine a direct lesion detection approach with secondary features such as the MPD diameter, thus indicating a promising avenue for the detection of pancreatic cancer at early stages.
Comparison of Medical Treatment Efficiency With Shear Wave Elastography Values of Thrombus in Patients With Lower Extremity Deep Vein Thrombosis
Authors: İnce Suat , Özgokçe Mesut , Özkaçmaz Sercan , Dündar İlyas , Türko Ensar , Ayyıldız Veysel A. , Göya Cemil 
Published: June 2023

Abstract
In lower-extremity deep vein thrombosis (DVT), thrombus age is essential for successful treatment. The aim of our study was to compare the shear wave elastography (SWE) values measured before treatment and achieved lumen patency after treatment in lower-extremity DVT patients with total occlusion. Patients diagnosed with DVT in the acute-subacute stage (<4 week) with total thrombosis in lower extremity were included in this prospective study. Shear wave elastography measurements were performed where the thrombus was most prominent and homogeneous. To evaluate patient response to treatment, lumen patency (partial [>25%] or total recanalization) was examined using color Doppler imaging in the first and third months posttreatment. Shear wave elastography values with and without patency were compared using an independent t test. Among 75 patients in this study, at the first-month color Doppler imaging examination, the SWE values were 1.77 ± 0.49 (1.09–3.03) m/s in patients who achieved lumen patency (n = 42) and 2.21 ± 0.54 (1.24–3.36) m/s in those who did not show lumen patency (n = 33). The difference between the groups' mean elastography value was statistically significant (P < 0.001). At the third-month examination, the SWE values were 1.76 ± 0.46 (1.09–3.03) m/s in patients with lumen patency (n = 55) and 2.52 ± 0.48 (1.74–3.36) in patients without lumen patency (n = 20). The difference between the 2 groups' mean elastography value was statistically significant (P < 0.001). We concluded that it is more difficult to achieve lumen patency in veins occluded by thrombus with higher elasto values, and endovascular interventional procedures should be considered during the initial treatment of high SWE value thrombosis.
Outcomes With Belatacept Exposure During Pregnancy in Kidney Transplant Recipients: A Case Series
Authors: Coscia Lisa , Cohen David , Dube Geoffrey K. , Hofmann R. Michael , Moritz Michael J. , Gattis Sara , Basu Arpita 
Published: June 2023

Background.
Posttransplant fertility returns quickly, and female recipients of child-bearing age may conceive while on immunosuppression. However, pregnancy after transplantation confers risks to the recipient, transplant, and fetus, including gestational hypertension, preeclampsia, gestational diabetes, transplant dysfunction, preterm labor, and low birthweight infants. Additionally, mycophenolic acid (MPA) products are teratogenic. Literature evidence regarding belatacept, a selective T-cell costimulation blocker, during pregnancy and while breastfeeding is extremely limited. When female transplant recipients on a belatacept-based regimen are desirous of pregnancy or at the time of conception, transplant providers manage the immunosuppression regimen in 1 of 2 ways: (1) switch both belatacept and MPA to a calcineurin inhibitor–based regimen with or without azathioprine, which is the more common practice but requires several modifications, having potential negative outcomes; or (2) only switch MPA to azathioprine while continuing belatacept.

Methods.
This case series includes 16 pregnancies in 12 recipients with exposure to belatacept throughout pregnancy and while breastfeeding. Patient information was obtained from several sources, including Transplant Pregnancy Registry International, providers at Emory University, and Columbia University, as well as literature review.

Results.
Pregnancy outcomes included 13 live births and 3 miscarriages. No birth defects or fetal deaths were reported in any of the live births. Seven infants were breastfed while their mothers continued belatacept. Outcomes appear comparable to those documented with the administration of calcineurin inhibitors.

Conclusions.
This case series provides data supporting the continued administration of belatacept during pregnancy. Additional research will assist in developing better guidelines to counsel female transplant recipients on belatacept desiring to pursue pregnancy.
Isolation and characterization of a novel glycoside hydrolase positive bacterial strain named Terrimonas ginsenosidimutans sp. nov. with ginsenoside-converting activity
Authors: Siddiqi Muhammad Zubair , Lee Ji Eun , Jun Min Ok , Huq Md. Amdadul , Im Wan-Taek 
Published: June 2023

A novel yellow-pigmented catalase- and oxidase-positive bacterial strain (designated NA20T) was isolated from wetland soil and characterized. Results of 16S rRNA and draft genome sequence analysis placed strain NA20T within the genus

Terrimonas

of the family

Chitinophagaceae

. Strain NA20T showed ≤97.1 % sequence similarity to members of the genus

Terrimonas

and the highest sequence similarity was found to

Terrimonas lutea

DYT (97.1%). The draft genome of strain NA20T had a total length of 7 144 125 base pairs. A total of 5659 genes were identified, of which 5613 were CDS and 46 RNA genes were assigned a putative function. Mining the genomes revealed the presence of 225 carbohydrate genes out of 1334 genes. Strain NA20T contained iso-C15 : 0, iso-C15 : 0 G, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) as major fatty acids. The predominant quinone was MK-7. The major polar lipids were phosphatidylethanolamine, one unknown polar lipid and one unknown aminophospholipid. Additionally, the functional analysis of NA20T showed the conversion of protopanaxatriol-mix type major ginsenosides (Rb1, Rc and Rd) to minor ginsenosides F2 and weak conversion of Rh2 and C-K within 24 h. As a result, the genotypic, phenotypic and taxonomic analyses support the affiliation of NA20T within the genus

Terrimonas

, for which the name Terrimonas ginsenosidimutans sp. nov. is proposed. The type strain is NA20T (=KACC 22218T=LMG 32198T).
DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters
Authors: Pham Tuan M. , Miffin Terrel , Sun Hongying , Sharp Kenneth K. , Wang Xiaoyu , Zhu Mingyi , Hoshika Shuichi , Peterson Raymond J. , Benner Steven A. , Kahn Jason D. , Mathews David H. 
Published: June 2023

ABSTRACTWe show thatin silicodesign of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1’-β-D-2’-deoxyribofuranosyl)-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one and 6-amino-3-(1’-β-D-2’-deoxyribofuranosyl)-5-nitro-(1H)-pyridin-2-one, simply P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit a new set of free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find that G-Z pairs have stability comparable to A-T pairs and therefore should be considered quantitatively by structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing with P-Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases where Eterna-player solutions were provided. P-Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P-Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.
Discrete Multiwalled Carbon Nanotubes for Versatile Intracellular Transport of Functional Biomolecular Complexes
Authors: Castillo Kevin , Tasset Aaron , Marinkovic Milos , Foote Aaron 
Published: June 2023

AbstractIn recent years, carbon nanotubes have emerged as a potentially revolutionary material with numerous uses in biomedical applications. Compared to other nanoparticles, discrete multi-walled carbon nanotubes (dMWCNTs) have been shown to exhibit advantageous characteristics such as high surface area to volume ratio, biocompatibility, and unique chemical and physical properties. dMWCNTs can be modified to load various molecules such as proteins and nucleic acids and are capable of crossing the cell membrane, making them attractive delivery vehicles for biomolecules. To investigate this, we measured the impact of dMWCNTs on cell proliferation. Furthermore, we used electron microscopy to demonstrate that dMWCNTs enter the cytoplasm of mammalian cells via an endocytosis-like process. And lastly, we employed variousin vitroreporter and gene assays to demonstrate dMWCNT-mediated delivery of peptides, mRNA, siRNA, and dsRNA. Our work here has helped further characterize dMWCNTs as a versatile delivery platform for biomolecular cargo.
Graded FGF activity patterns distinct cell types within the apical sensory organ of the sea anemoneNematostella vectensis
Authors: Sabin Keith Z. , Chen Shiyuan , Hill Eric , Weaver Kyle J. , Yonker Jacob , Kirkman MaryEllen , Redwine Bret , Klompen Anna M. L. , Zhao Xia , Guo Fengli , McKinney Cathy , Dewey Jessica L. , Gibson Matthew C. 
Published: June 2023

AbstractBilaterian animals have evolved complex sensory organs comprised of distinct cell types that function coordinately to sense the environment. Each sensory unit has a defined architecture built from component cell types, including sensory cells, non-sensory support cells, and dedicated sensory neurons. Whether this characteristic cellular composition is present in the sensory organs of non-bilaterian animals is unknown. Here, we interrogate the cell type composition and gene regulatory networks controlling development of the larval apical sensory organ in the sea anemoneNematostella vectensis. Using single cell RNA sequencing and imaging approaches, we reveal two unique cell types in theNematostellaapical sensory organ, GABAergic sensory cells and a putative non-sensory support cell population. Further, we identify the paired-like (PRD) homeodomain geneprd146as a specific sensory cell marker and show that Prd146+sensory cells become post-mitotic after gastrulation. Genetic loss of function approaches show that Prd146 is essential for apical sensory organ development. Using a candidate gene knockdown approach, we placeprd146downstream of FGF signaling in the apical sensory organ gene regulatory network. Further, we demonstrate that an aboral FGF activity gradient coordinately regulates the specification of both sensory and support cells. Collectively, these experiments define the genetic basis for apical sensory organ development in a non-bilaterian animal and reveal an unanticipated degree of complexity in a prototypic sensory structure.
Cotyledon Peeling Method for Passion Fruit Protoplasts: a versatile cell system for transient gene expression in passion fruit (Passiflora edulis)
Authors: Wang Linxi , Liu Haobin , Liu Peilan , Wu Guanwei , Shen Wentao , Cui Hongguang , Dai Zhaoji 
Published: June 2023

AbstractPassion fruit (Passiflora edulis) is a perennial evergreen vine that grows mainly in tropical and subtropical regions due to its nutritional, medicinal and ornamental values. However, the molecular biology study of passion fruit is extremely hindered by the lack of an easy and efficient method for transformation. The protoplast transformation system plays a vital role in plant regeneration, gene function analysis and genome editing. Here, we present a new method (‘Cotyledon Peeling Method’) for simple and efficient passion fruit protoplast isolation using cotyledon as the source tissue. A high yield (2.3 × 107protoplasts per gram of fresh tissues) and viability (76%) of protoplasts were obtained upon incubation in the enzyme solution [1% (w/v) cellulase R10, 0.25% (w/v) macerozyme R10, 0.4 M mannitol, 10 mM CaCl2, 20 mM KCl, 20 mM MES and 0.1% (w/v) BSA, pH 5.7] for 2 hours. In addition, we achieved high transfection efficiency of 83% via the polyethylene glycol (PEG)-mediated transformation with a green fluorescent protein (GFP)-tagged plasmid upon optimization. The crucial factors affecting transformation efficiency were optimized as follows: 3 μg of plasmid DNA, 5 min transfection time, PEG concentration at 40% and protoplast density of 100 × 104cells/ml. Furthermore, the established protoplast system was successfully applied for subcellular localization analysis of multiple fluorescent organelle markers and protein-protein interaction study. Taken together, we report a simple and efficient passion fruit protoplast isolation and transformation system, and demonstrate its usage in transient gene expression for the first time in passion fruit. The protoplast system would provide essential support for various passion fruit biology studies, including genome editing, gene function analysis and whole plant regeneration.
Analysts' identity negotiations and politeness behaviour in earnings calls of US firms with extreme earnings changes
Authors: Koller Veronika , Wu Xiaoxi 
Published: June 2023

PurposeFinancial analysts' roles and incentives mean that they have conflicting identities to maintain towards investors and firm managers. The authors study how analysts adopt various politeness strategies in their questioning to establish socially desirable identities in the Q&A of publicly accessible earnings calls.Design/methodology/approachThe study is based on a sample of US firms with extreme earnings changes. 46 transcripts of end-of-year earnings calls were investigated with the help of linguistic discourse analysis, drawing on frameworks of face and linguistic politeness. For each transcript, the authors identified the structure of the face-threatening acts (FTAs) that arise when analysts ask probing questions and ascertained what specific politeness strategies, if any, are used by analysts to mitigate those FTAs. The authors examine how analysts perform identities through politeness in language and compare analysts' politeness behaviour and identity construction in the increasing earnings sub-sample with the decreasing earnings sub-sample.FindingsAnalysts negotiate different identities according to specific social contexts, promoting their identity as (1) competent professionals when firms report problematic performance by asking questions in a confrontational manner with few politeness strategies and (2) dependents of the firm by asking questions in a more polite manner when firms experience satisfactory performance. Analysts aim to present a socially desirable face in Q&A to influence managers' and investors' perceptions.Practical implicationsThe study raises awareness about linguistic politeness as a communication strategy in the Q&A in earnings calls. It thereby enables managers and analysts to use linguistic politeness consciously and strategically and to recognise such use by others.Originality/valueThis study complements existing literature on earnings conference calls as part of external corporate communications by focusing on analysts' use of language when interacting with manages. To the best of our knowledge, this paper is the first to show that politeness underpins analysts' language use as a device for identity negotiations. This is important to understand because analysts' identities vis-a-vis managers and investors is closely related to the stability of the financial system.
Random vibration-based virtual fatigue test for large-scale welded structures using frequency-domain structural stress method and its application to traction transformers
Authors: Tang Zimou , Yang Min , Xiao Jianxiong , Shen Zheng , Tang Liming , Wang Jibin 
Published: June 2023

PurposeThis paper aims to present an engineering computational method for fatigue life evaluation of welded structures on large-scale equipment under random vibration load.Design/methodology/approachBased on a case study of the traction transformers, virtual fatigue test (VFT) was proposed via numerical simulation approach. Static analysis was conducted to identify the risky zone and then dynamic response of the risky welds under random vibration load was calculated based on frequency-domain structural stress method (FDSSM) theory, life distribution and associated survivability at various locations of the structure were obtained. Structural modification was finally performed according to the evaluation results. Moreover, experimental test was carried out and compared with the virtual test result.FindingsBy applying the virtual test, fatigue life of the complex welded structures on large-scale equipment can be accurately and efficiently obtained considering dynamic effect under random vibration load. Meanwhile, risky welds can be directly determined and targeted modification scheme can be accordingly concluded. Validity of the VFT result was proved by comparing with the experimental test.Originality/valueThe proposed method can help obtain equivalent structural stress and fatigue life distribution of the welded structure at any position with various survivability and make quantitative evaluation on the life-extending effect of the structural modification. This method shows significant cost and efficiency advantages over experimental test during design stage of the large-scale structures in numerous manufacturing industries.