bluuebunny/crossref_metadata_2025 huggingface dataset:
CLOVES syndrome and cervical arteriovenous fistula: a unique association managed by combined microsurgical and endovascular therapy
Authors: Alhazzab Alhanouf , Alkhaibary Ali , Khairy Sami , Alshaya Wael
Published: March 2021

CLOVES syndrome is a condition characterized by congenital lipomatous overgrowth, vascular malformations, epidermal nevi and skeletal anomalies. The association of cervical arteriovenous fistula with CLOVES syndrome is extremely rare. To the best of our knowledge, only two cases were reported in the literature. We hereby report an additional case and review the literature on this condition. A 12-year-old girl, known to have CLOVES syndrome, presented to the emergency department with a 2-week history of bilateral, progressive lower extremity and left arm weakness. Radiological imaging demonstrated a C3–C6 left extradural lesion, containing multiple enhancing vessels, causing marked compression on the spinal cord. Urgent spinal decompression was performed, with C3–C6 instrumentation, followed by a two-stage embolization of the fistula. Cervical arteriovenous fistula can be rarely identified in patients with CLOVES syndrome. High index of suspicion is required to promptly evaluate patients with CLOVES syndrome presenting with new-onset neurological deficits.
Annular pancreas causing pyloric stenosis in a 66-year-old patient treated with gastrojejunostomy: a case report
Authors: Patel P , Diko S , Kulkarni S , Persaud C , Sartorato F , Christian D
Published: March 2021

Annular pancreas is defined by a ring of pancreatic tissue encircling the descending portion of the duodenum. It is exceptionally rare in adults and commonly diagnosed during the investigation of symptoms arising due to its complications. Treatment usually involves the surgical correction with a duodenoduodenostomy, gastrojejunostomy or duodenojejunostomy. We discuss the case of a 66-year-old male patient who presented with symptoms of gastric outlet obstruction and was found to have an annular pancreas encircling the pylorus and the first and second portions of the duodenum and was treated by performing a gastrojejunostomy. Upper gastrointestinal series, computerized tomography (CT) scans, and magnetic resonance cholangeopancreatographys can all be used for preoperative diagnosis; however, endoscopic retrograde cholangiopancreatography (ERCP) is the diagnostic modality of choice. Nonetheless, many patients may only be diagnosed intraoperatively, especially those who cannot undergo an ERCP due to stenosis proximal to the duodenum or patients in whom the annulus may not be visible on CT scan.
Encrypted Citations: The Bondwoman’s Narrative and the Case of Jane Johnson
Authors: Barter Faith
Published: March 2021

I read Hannah Crafts’s The Bondwoman’s Narrative (2002) and its legal historical intertexts in order to nuance “fiction” as a literary category of antebellum African American writing. Specifically, I develop connections between The Bondwoman’s Narrative and US laws of slavery by thinking about the novel’s form in relation to legal citational practices. I argue that the novel encrypts and encodes legal narratives within its fictionalized accounts of verifiable “historical” events. By close reading Crafts’s alterations of such events, I compare her use of encryption to the citational practices inherent in legal precedent. This comparison yields a stronger understanding of antebellum African American authorial practices as deploying legal rhetorical strategies that resisted dominant legal narratives and generated new literary forms. I problematize the tendency to redeem law as a possible or ideal site of black belonging and to underscore the ways that authors such as Crafts encrypted their writing with rejections of law and the nation-state. Her work does so even as it rehearses a facility and engagement with legal culture that might suggest an effort to inscribe African Americans into legal frameworks and the ongoing nineteenth-century project of US nation-building. Instead of reading this complex engagement with US law as evincing an attachment to it, I argue for reading it as the rejection and radical reimagining of existing logics of authority and community.
Characterizing the magnetic fields of nearby molecular clouds using submillimeter polarization observations
Authors: Sullivan Colin H , Fissel L M , King P K , Chen C-Y , Li Z-Y , Soler J D
Published: March 2021

Of all the factors that influence star formation, magnetic fields are perhaps the least well understood. The goal of this paper is to characterize the 3D magnetic field properties of nearby molecular clouds through various methods of statistically analysing maps of polarized dust emission. Our study focuses on nine clouds, with data taken from the Planck Sky Survey as well as data from the Balloon-borne Large Aperture Submillimeter Telescope for Polarimetry observations of Vela C. We compare the distributions of polarization fraction (p), dispersion in polarization angles ($\mathcal {S}$), and hydrogen column density (NH) for each of our targeted clouds. To broaden the scope of our analysis, we compare the distributions of our clouds’ polarization observables with measurements from synthetic polarization maps generated from numerical simulations. We also use the distribution of polarization fraction measurements to estimate the inclination angle of each cloud’s cloud-scale magnetic field. We obtain a range of inclination angles associated with our clouds, varying from 16○ to 69○. We establish inverse correlations between p and both $\mathcal {S}$ and NH in almost every cloud, but we are unable to establish a statistically robust $\mathcal {S}$ versus NH trend. By comparing the results of these different statistical analysis techniques, we are able to propose a more comprehensive view of each cloud’s 3D magnetic field properties. These detailed cloud analyses will be useful in the continued studies of cloud-scale magnetic fields and the ways in which they affect star formation within these molecular clouds.
Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters
Authors: Shen Yuning , Pressman Abe , Janzen Evan , Chen Irene A
Published: March 2021

Characterizing genotype-phenotype relationships of biomolecules (e.g. ribozymes) requires accurate ways to measure activity for a large set of molecules. Kinetic measurement using high-throughput sequencing (e.g. k-Seq) is an emerging assay applicable in various domains that potentially scales up measurement throughput to over 106 unique nucleic acid sequences. However, maximizing the return of such assays requires understanding the technical challenges introduced by sequence heterogeneity and DNA sequencing. We characterized the k-Seq method in terms of model identifiability, effects of sequencing error, accuracy and precision using simulated datasets and experimental data from a variant pool constructed from previously identified ribozymes. Relative abundance, kinetic coefficients, and measurement noise were found to affect the measurement of each sequence. We introduced bootstrapping to robustly quantify the uncertainty in estimating model parameters and proposed interpretable metrics to quantify model identifiability. These efforts enabled the rigorous reporting of data quality for individual sequences in k-Seq experiments. Here we present detailed protocols, define critical experimental factors, and identify general guidelines to maximize the number of sequences and their measurement accuracy from k-Seq data. Analogous practices could be applied to improve the rigor of other sequencing-based assays.
Diagnostic Utility of a Ferritin-to-Procalcitonin Ratio to Differentiate Patients With COVID-19 From Those With Bacterial Pneumonia: A Multicenter Study
Authors: Gharamti Amal A , Mei Fei , Jankousky Katherine C , Huang Jin , Hyson Peter , Chastain Daniel B , Fan Jiawei , Osae Sharmon , Zhang Wayne W , Montoya José G , Erlandson Kristine M , Scherger Sias J , Franco-Paredes Carlos , Henao-Martínez Andrés F , Shapiro Leland
Published: March 2021

Background

There is an urgent need for accurate, rapid, inexpensive biomarkers that can differentiate coronavirus disease 2019 (COVID-19) from bacterial pneumonia. We assess the role of the ferritin-to-procalcitonin (F/P) ratio to classify pneumonia cases into those due to COVID-19 vs those due to bacterial pathogens.

Methods

This multicenter case–control study compared patients with COVID-19 with those with bacterial pneumonia, admitted between March 1 and May 31, 2020. Patients with COVID-19 and bacterial pneumonia co-infection were excluded. The F/P in patients with COVID-19 vs with bacterial pneumonia were compared. Receiver operating characteristic curve analysis determined the sensitivity and specificity of various cutoff F/P values for COVID-19 vs bacterial pneumonia.

Results

A total of 242 COVID-19 pneumonia cases and 34 bacterial pneumonia controls were included. Patients with COVID-19 pneumonia had a lower mean age (57.1 vs 64.4 years; P = .02) and a higher body mass index (30.74 vs 27.15 kg/m2; P = .02) compared with patients with bacterial pneumonia. Cases and controls had a similar proportion of women (47% vs 53%; P = .5), and COVID-19 patients had a higher prevalence of diabetes mellitus (32.6% vs 12%; P = .01). The median F/P was significantly higher in patients with COVID-19 (4037.5) compared with the F/P in bacterial pneumonia (802; P < .001). An F/P ≥877, used to diagnose COVID-19, resulted in a sensitivity of 85% and a specificity of 56%, with a positive predictive value of 93.2% and a likelihood ratio of 1.92. In multivariable analyses, an F/P ≥877 was associated with greater odds of identifying a COVID-19 case (odds ratio, 11.27; 95% CI, 4–31.2; P < .001).

Conclusions

An F/P ≥877 increases the likelihood of COVID-19 pneumonia compared with bacterial pneumonia.
Antimicrobial Time-Out for Vancomycin by Infectious Disease Physicians Versus Clinical Pharmacists: A Before-After Crossover Trial
Authors: Hasegawa Shinya , Tagashira Yasuaki , Murakami Shutaro , Urayama Yasunori , Takamatsu Akane , Nakajima Yuki , Honda Hitoshi
Published: March 2021

Background

The present study assessed the impact of time-out on vancomycin use and compared the strategy’s efficacy when led by pharmacists versus infectious disease (ID) physicians at a tertiary care center.

Methods

Time-out, consisting of a telephone call to inpatient providers and documentation of vancomycin use >72 hours, was performed by ID physicians and clinical pharmacists in the Departments of Medicine and Surgery/Critical Care. Patients in the Department of Medicine were assigned to the clinical pharmacist-led arm, and patients in the Department of Surgery/Critical Care were assigned to the ID physician-led arm in the initial, 6-month phase and were switched in the second, 6-month phase. The primary outcome was the change in weekly days of therapy (DOT) per 1000 patient-days (PD), and vancomycin use was compared using interrupted time-series analysis.

Results

Of 587 patients receiving vancomycin, 132 participated, with 79 and 53 enrolled in the first and second phases, respectively. Overall, vancomycin use decreased, although the difference was statistically nonsignificant (change in slope, −0.25 weekly DOT per 1000 PD; 95% confidence interval [CI], −0.68 to 0.18; P = .24). The weekly vancomycin DOT per 1000 PD remained unchanged during phase 1 but decreased significantly in phase 2 (change in slope, −0.49; 95% CI, −0.84 to −0.14; P = .007). Antimicrobial use decreased significantly in the surgery/critical care patients in the pharmacist-led arm (change in slope, −0.77; 95% CI, −1.33 to −0.22; P = .007).

Conclusions

Vancomycin time-out was moderately effective, and clinical pharmacist-led time-out with surgery/critical care patients substantially reduced vancomycin use.
New Challenger Parties in Opposition: Isolation or Cooperation?
Authors: De Giorgi Elisabetta , Dias António , Dolný Branislav
Published: March 2021

The context of European parties has been through a process of significant transformation in recent years, with the fall of traditional mainstream parties and the rise of challenger parties. Despite their significant differences, mainly at the ideological level, we argue that challenger parties share some common characteristics when they first enter parliament. Namely, we expect them to employ a similar strategy as regards their relationship with the other party actors and to attempt to send the same message to their electorate: that they represent the alternative to existing parties, be it in government or in opposition, and will behave accordingly in parliament. We test our expectations by analysing and comparing the cooperation attitudes of challenger parties vis-à-vis the other opposition parties, using legislative co-sponsorship during their first term in parliament as an indicator and Social Network Analysis as a method.
Can Opposition Parties Be Responsible?
Authors: Ilonszki Gabriella , Marangoni Francesco , Palau Anna M
Published: March 2021

Opposition responsibility is a neglected field, and if at all noticed, opposition parties are often placed in the irresponsibility frame. The purpose of our paper is to examine to what extent, under which conditions, and in which ways opposition parties can be considered to act responsibly. This article will develop the concept of opposition responsibility and test the expectations in the behaviour of opposition parties in three countries: Hungary, Italy and Spain. The analysis highlights that opposition responsibility exceeds—although does not exclude—policy making and scrutiny activities as it has broader implications. We shall regard the opposition’s general performance and their political system-related behaviour as components of responsibility.
Manipulating ZmEXPA4 expression ameliorates the drought-induced prolonged anthesis and silking interval in maize
Authors: Liu Boxin , Zhang Bin , Yang Zhirui , Liu Yan , Yang Shiping , Shi Yunlu , Jiang Caifu , Qin Feng
Published: March 2021

Drought poses a major environmental threat to maize (Zea mays) production worldwide. Since maize is a monoecious plant, maize grain yield is dependent on the synchronous development of male and female inflorescences. When a drought episode occurs during flowering, however, an asynchronism occurs in the anthesis and silking interval (ASI) that results in significant yield losses. The underlying mechanism responsible for this asynchronism is still unclear. Here, we obtained a comprehensive development-drought transcriptome atlas of maize ears. Genes that function in cell expansion and growth were highly repressed by drought in 50 mm ears. Notably, an association study using a natural-variation population of maize revealed a significant relationship between the level of α-expansin4 (ZmEXPA4) expression and drought-induced increases in ASI. Furthermore, genetic manipulation of ZmEXPA4 expression using a drought-inducible promoter in developing maize ears reduced the ASI under drought conditions. These findings provide important insights into the molecular mechanism underlying the increase in ASI in maize ears subjected to drought and provide a promising strategy that can be used for trait improvement.
The Arabidopsis MATERNAL EFFECT EMBRYO ARREST45 protein modulates maternal auxin biosynthesis and controls seed size by inducingAINTEGUMENTA
Authors: Li Ying Ju , Yu Yang , Liu Xiuying , Zhang Xian Sheng , Su Ying Hua
Published: March 2021

Seed size is a major factor determining crop yields that is controlled through the coordinated development of maternal and zygotic tissues. Here, we identified Arabidopsis MATERNAL EFFECT EMBRYO ARREST45 (MEE45) as a B3 transcription factor that controls cell proliferation and maternally regulates seed size through its transcriptional activation of AINTEGUMENTA (ANT) and its downstream control of auxin biosynthesis in the ovule integument. After characterizing reduced seed and organ size phenotypes in mee45 mutants and finding that overexpression of MEE45 causes oversized seeds, we discovered that the MEE45 protein can bind to the promoter region of the ANT locus and positively regulate its transcription. ANT in-turn activates the expression of auxin biosynthetic genes (e.g. YUCCA4) in the ovule integument. Our results thus illustrate mechanisms underlying maternal tissue-mediated regulation of seed size and suggest that MEE45 and its downstream components can be harnessed to develop higher-yielding crop varieties.
AUXIN RESPONSE FACTOR 18–HISTONE DEACETYLASE 6 module regulates floral organ identity in rose (Rosa hybrida)
Authors: Chen Jiwei , Li Yang , Li Yonghong , Li Yuqi , Wang Yi , Jiang Chuyan , Choisy Patrick , Xu Tao , Cai Youming , Pei Dong , Jiang Cai-Zhong , Gan Su-Sheng , Gao Junping , Ma Nan
Published: March 2021

The phytohormone auxin plays a pivotal role in floral meristem initiation and gynoecium development, but whether and how auxin controls floral organ identity remain largely unknown. Here, we found that auxin levels influence organ specification, and changes in auxin levels influence homeotic transformation between petals and stamens in rose (Rosa hybrida). The PIN-FORMED-LIKES (PILS) gene RhPILS1 governs auxin levels in floral buds during floral organogenesis. RhAUXIN RESPONSE FACTOR 18 (RhARF18), whose expression decreases with increasing auxin content, encodes a transcriptional repressor of the C-class gene RhAGAMOUS (RhAG), and controls stamen–petal organ specification in an auxin-dependent manner. Moreover, RhARF18 physically interacts with the histone deacetylase (HDA) RhHDA6. Silencing of RhHDA6 increases H3K9/K14 acetylation levels at the site adjacent to the RhARF18-binding site in the RhAG promoter and reduces petal number, indicating that RhARF18 might recruit RhHDA6 to the RhAG promoter to reinforce the repression of RhAG transcription. We propose a model for how auxin homeostasis controls floral organ identity via regulating transcription of RhAG
Photooxidation crosslinking to recover residual stress in decellularized blood vessel
Authors: Wang Jintao , Kong Lingwen , Gafur Alidha , Peng Xiaobo , Kristi Natalia , Xu Jing , Ma Xingshuang , Wang Nan , Humphry Rose , Durkan Colm , Zhang Haijun , Ye Zhiyi , Wang Guixue
Published: March 2021

Decellularization method based on trypsin-digestion is widely used to construct small diameter vascular grafts. However, this method will reduce the opening angle of the blood vessel and result in the reduction of residual stress. Residual stress reduced has an adverse effect on the compliance and permeability of small diameter vascular grafts. To improve the situation, acellular blood vessels were treated with glutaraldehyde and photooxidation crosslinking respectively, and the changes of opening angle, circumferential residual strain of native blood vessels, decellularized arteries and crosslinked blood vessels were measured by means of histological examination, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) in this study. The opening angle of decellularized arteries significantly restored after photooxidation crosslinking (P = 0.0216), while that of glutaraldehyde crosslinking blood vessels reduced. The elastic fibers inside the blood vessels became densely rearranged after photooxidation crosslinking. The results of finite element simulation showed that the residual stress increased with the increase of opening angle. In this study, we found at the first time that photooxidation crosslinking method could significantly increase the residual stress of decellularized vessels, which provides biomechanical support for the development of new biomaterials of vascular grafts.
Biological evaluations of decellularized extracellular matrix collagen microparticles prepared based on plant enzymes and aqueous two-phase method
Authors: Liu YaWen , Huang Ching-Cheng , Wang YuanYuan , Xu Jun , Wang GuoDing , Bai XinPeng
Published: March 2021

For patients with extensive full-thickness burns who do not have sufficient autologous split-thickness skin for skin grafts, the application of biological skin substitutes may be considered. The aim of this study was to find an optimal new type method for the production of a biovital skin substitute based on acellular dermal matrix (ADM) and preclinical evaluations. In this work, 25 methods of ADM production were assessed. The proposed methods are based on the use of the following enzymes: papain, Carica papaya lipase (CPL), and purification using a polymer/salt aqueous two-phase system. The obtained ADM samples were characterized via scanning electron microscopy (SEM), porosity measurement and water vapor transmission test. Results showed that the collagen bundles of ADM microparticles were intact and orderly. Through differential scanning calorimetry (DSC), thermo gravimetric analysis (TGA) and biocompatibility tests, the results indicated that the proportion of papain and CPL was the same and 5 h processing time are the optimum conditions for ADM preparation and the material showed good biocompatibility. Our results suggested that the potential of developing this kind of decellularization process to manufacture ADM scaffolds for clinical application.
Antioxidant biocompatible composite collagen dressing for diabetic wound healing in rat model
Authors: Qian Bei , Li Jialun , Guo Ke , Guo Nengqiang , Zhong Aimei , Yang Jie , Wang Jiecong , Xiao Peng , Sun Jiaming , Xiong Lingyun
Published: March 2021

Associated with persistent oxidative stress, altered inflammatory responses, poor angiogenesis and epithelization, wound healing in diabetic patients is impaired. N-acetylcysteine (NAC) is reported to resist excess reactive oxygen species (ROS) production, prompt angiogenesis and maturation of the epidermis. Studies have revealed that graphene oxide (GO) can regulate cellular behavior and form cross-links with naturally biodegradable polymers such as collagen (COL) to construct composite scaffolds. Here, we reported a COL-based implantable scaffold containing a mixture of GO capable of the sustained delivery of NAC to evaluate the wound healing in diabetic rats. The morphological, physical characteristics, biocompatibility and NAC release profile of the GO-COL-NAC (GCN) scaffold were evaluated in vitro. Wound healing studies were performed on a 20 mm dorsal full-skin defect of streptozotocin (STZ)-induced diabetic rats. The injured skin tissue was removed at the 18th day post-surgery for histological analysis and determination of glutathione peroxidase (GPx), catalase (CAT) and superoxide dismutase (SOD) activity. In diabetic rats, we confirmed that the GCN scaffold presented a beneficial effect in enhancing the wound healing process. Additionally, due to the sustained release of NAC, the scaffold may potentially induce the antioxidant defense system, upregulating the expression levels of the antioxidant enzymes in the wound tissue. The findings revealed that the antioxidant biocompatible composite collagen dressing could not only deliver NAC in situ for ROS inhibition but also promote the wound healing process. This scaffold with valuable therapy potential might enrich the approaches for surgeon in diabetic wound treatment in the future.
Tuning filament composition and microstructure of 3D-printed bioceramic scaffolds facilitate bone defect regeneration and repair
Authors: Chen Yi , Huang Jiaping , Liu Jiamei , Wei Yingming , Yang Xianyan , Lei Lihong , Chen Lili , Wu Yanmin , Gou Zhongru
Published: March 2021

It is still a challenge to optimize the component distribution and microporous structures in scaffolds for tailoring biodegradation (ion releasing) and enhancing bone defect repair within an expected time stage. Herein, the core–shell-typed nonstoichiometric wollastonite (4% and 10% Mg-doping calcium silicate; CSiMg4, CSiMg10) macroporous scaffolds with microporous shells (adding ∼10 μm PS microspheres into shell-layer slurry) were fabricated via 3D printing. The initial mechanical properties and bio-dissolution (ion releasing) in vitro, and osteogenic capacity in vivo of the bioceramic scaffolds were evaluated systematically. It was shown that endowing high-density micropores in the sparingly dissolvable CSiMg10 or dissolvable CSiMg4 shell layer inevitably led to nearly 30% reduction of compressive strength, but such micropores could readily tune the ion release behaviour of the scaffolds (CSiMg4@CSiMg10 vs. CSiMg4@CSiMg10-p; CSiMg10@CSiMg4 vs. CSiMg10@CSiMg4-p). Based on the in rabbit femoral bone defect repair model, the 3D μCT reconstruction and histological observation demonstrated that the CSiMg4@CSiMg10-p scaffolds displayed markedly higher osteogenic capability than the other scaffolds after 12 weeks of implantation. It demonstrated that core–shell bioceramic 3D printing technique can be developed to fabricate single-phase or biphasic bioactive ceramic scaffolds with accurately tailored filament biodegradation for promoting bone defect regeneration and repair in some specific pathological conditions.
Autologous haematopoietic stem cell transplantation restores the suppressive capacity of regulatory B cells in systemic sclerosis patients
Authors: Lima-Júnior João R , Arruda Lucas C M , Gonçalves Maynara S , Dias Juliana B E , Moraes Daniela A , Covas Dimas T , Simões Belinda P , Oliveira Maria Carolina , Malmegrim Kelen C R
Published: March 2021

Objectives

The rationale of autologous haematopoietic stem cell transplantation (AHSCT) for autoimmune diseases is that high-dose immunosuppression eradicates autoreactive T and B cells and the infused autologous haematopoietic stem cells promote reconstitution of a naïve and self-tolerant immune system. The aim of this study was to evaluate the reconstitution of different B cell subsets, both quantitatively and functionally, in SSc patients treated with AHSCT.

Methods

Peripheral blood was harvested from 22 SSc patients before transplantation and at 30, 60, 120, 180 and 360 days post-AHSCT. Immunophenotyping of B cell subsets, B cell cytokine production, signalling pathways and suppressive capacity of regulatory B cells (Bregs) were assessed by flow cytometry.

Results

Naïve B cell frequencies increased from 60 to 360 days post-AHSCT compared with pre-transplantation. Conversely, memory B cell frequencies decreased during the same period. Plasma cell frequencies transiently decreased at 60 days post-AHSCT. IL-10-producing Bregs CD19+CD24hiCD38hi and CD19+CD24hiCD27+ frequencies increased at 180 days. Moreover, the phosphorylation of extracellular signal-regulated kinase 1/2 and p38 mitogen-activated protein kinase increased in B cells reconstituted post-AHSCT. Notably, CD19+CD24hiCD38hi Bregs recovered their ability to suppress production of Th1 cytokines by CD4+ T cells at 360 days post-AHSCT. Finally, IL-6 and TGF-β1-producing B cells decreased following AHSCT.

Conclusion

Taken together, these results suggest improvements in immunoregulatory and anti-fibrotic mechanisms after AHSCT for SSc, which may contribute to re-establishment of self-tolerance and clinical remission.
Adaptation and withdrawal of feeding dried Aspergillus oryzae fermentation product to dairy cattle and goats on in vitro NDF digestibility of selected forage sources
Authors: Hymes-Fecht Ursula C , Casper David P
Published: March 2021

Nutritional fermentation aids [dried Aspergillus oryzae fermentation product (AO)] are used in livestock production to increase nutrient digestion and production efficiency. The objective was to determine AO impact on neutral detergent fiber (NDF) degradation of selected forage sources (FS). A series of in vitro fermentation experiments were conducted using rumen fluid (RF) from rumen fistulated dairy heifers or dairy goats evaluating AO at 0.0, 0.3, or 0.6 g/L inclusion rates. In experiment I, the optimum AO concentration using alfalfa hay (AH), Bermuda grass (BG) hay, and peanut skins (PS) was determined via 48-h in vitro neutral detergent fiber digestion (IVNDFd). In experiment II, 0.0 g/L and 0.3 g/L AO were used to determine in vitro dry matter digestion (IVDMD), in vitro organic matter digestion (IVOMD), IVNDFd, and NDF digestion kinetics. In experiment III, in vivo AO ruminal adaptation (AD) and withdrawal (WD) times were determined for both dairy heifers and goats on IVDMD, IVOMD, IVNDFd, and NDF digestion kinetics. In experiment I, IVNDFd was similar using RF from dairy heifers or goats with IVNDFd being increased 10%, 28%, and 23% for AH, BG, and PS, respectively, at 0.3 g/L of AO compared with 0.0 g/L AO, while adding 0.6 g/L AO reduced IVNDFd among all FS. In experiment II, IVNDFd was greater when adding 0.0 g/L AO compared with 0.3 g/L AO using dairy goat RF (26.7% and 37.6%, respectively) among all FS. The mean retention time and 50% digestion times were greater, while digestion rate was lower for PS compared to AH and BG. In vitro dry matter (DM) and organic matter (OM) digestibilities were greater with AO for AH and BG compared to PS but varied with RF donor source. In experiment III, in vitro DM digestibility increased then decreased with adaptation time, while AO withdrawal increased digestion of DM, OM, and NDF. The NDF digestion kinetics were similar across all FS (AH, BG, and PS), which resulted in no clear determination of AO adaptation and withdrawal times needed for AO efficacy. The optimal AO inclusion rate was determined to be 0.3 g/L for improving in vitro NDF digestion, but subsequent experiments could not confirm that inclusion rate. Inclusion rates greater than 0.3 g/L depressed NDF degradation, which should be avoided due to depression of NDF digestion. Sourcing ruminal fluid from dairy heifers or goats for conducting in vitro fermentations resulted in similar DM, OM, and NDF digestion and NDF degradation kinetics.
MicroRNA‐191‐5p ameliorates amyloid‐β1‐40–mediated retinal pigment epithelium cell injury by suppressing the NLRP3 inflammasome pathway
Authors: Chen Jieqiong , Sun Junran , Hu Yifan , Wan Xiaoling , Wang Yuwei , Gao Min , Liang Jian , Liu Te , Sun Xiaodong
Published: March 2021

Amyloid β (Aβ) is a crucial component of drusen, the hallmark of the early stage of age‐related macular degeneration (AMD), and can cause retinal pigment epithelium (RPE) cell damage through activation of the inflammatory response. MicroRNAs play a critical role in inflammation. However, the mechanism underlying the effect of microRNAs on the NLRP3 inflammasome induced by Aβ remains poorly understood. In the present study, we demonstrated that Aβ1‐40‐mediated RPE damage by inducing a decrease in endogenous miR‐191‐5p expression. This led to the upregulation of its target gene, C/EBPβ. C/EBPβ acts as a transcription factor for NLRP3, promotes its transcription, and upregulates the downstream inflammatory factors Caspase‐1 and IL‐1β. Correspondingly, overexpression of miR‐191‐5p alleviated RPE cell injury by suppressing inflammation. The present study elucidates a novel transcriptional regulatory mechanism of the NLRP3 inflammasome. Our findings suggest an anti‐inflammatory effect of miR‐191‐5p in Aβ1‐40‐induced RPE impairment, shedding light on novel preventive or therapeutic approaches for AMD‐associated RPE impairment.
ATM inhibitor KU‐55933 induces apoptosis and inhibits motility by blocking GLUT1‐mediated glucose uptake in aggressive cancer cells with sustained activation of Akt
Authors: Harris Benjamin R. E. , Zhang Ye , Tao Jianxin , Shen Renhui , Zhao Xiaoqian , Cleary Margot P. , Wang Tong , Yang Da‐Qing
Published: March 2021

Enhanced glucose uptake is coupled with elevated aerobic glycolysis (the Warburg effect) in cancer cells and is closely correlated with increased tumor aggressiveness and poor prognosis. We previously discovered that ATM, a protein kinase deficient in Ataxia‐telangiectasia (A‐T) disease, is an insulin‐responsive protein that participates in insulin‐mediated glucose uptake in muscle cells by stimulating glucose transporter 4 (GLUT4) translocation. However, the role of ATM in glucose uptake and tumorigenesis of cancer cells is unclear. In the present study, we found that aggressive breast and prostate cancer cell lines with overactivated Akt activity exhibit enhanced glucose uptake and GLUT1 translocation upon insulin treatment, and KU‐55933, a specific inhibitor of ATM, inhibits insulin‐mediated glucose uptake by blocking translocation of GLUT1 to the cell surface. KU‐55933 also inhibits aerobic glycolysis and ATP production in these cells. Moreover, KU‐55933 induces apoptosis and inhibits motility of cancer cells by inhibiting glucose uptake. Our results showed that while high concentration of glucose and insulin promote the expression of a mesenchymal biomarker (vimentin) in these cancer cells, KU‐55933 strongly inhibits its expression as well as epithelial to mesenchymal transition. The roles of ATM in stimulating glucose uptake, glycolysis, motility, and proliferation of cancer cells were demonstrated by knocking‐down ATM in these cells. KU‐55933 treatment also inhibits tumor growth and metastasis in vivo in mouse mammary tumors through inhibition of GLUT1 translocation and vimentin expression. These results suggest that ATM acts as a promoter of tumorigenesis in cancer cells with overactivated Akt, and KU‐55933 induces apoptosis and inhibits motility by blocking GLUT1‐mediated glucose uptake and glycolysis in these cancer cells, which may lead to the use of KU‐55933 and its analogs as new preventive or therapeutic agents against cancer.
Hypoxia‐inducible factor‐dependent induction of myeloid‐derived netrin‐1 attenuates natural killer cell infiltration during endotoxin‐induced lung injury
Authors: Berg Nathaniel K. , Li Jiwen , Kim Boyun , Mills Tingting , Pei Guangsheng , Zhao Zhongming , Li Xiangyun , Zhang Xu , Ruan Wei , Eltzschig Holger K. , Yuan Xiaoyi
Published: March 2021

Sepsis and sepsis‐associated lung inflammation significantly contribute to the morbidity and mortality of critical illness. Here, we examined the hypothesis that neuronal guidance proteins could orchestrate inflammatory events during endotoxin‐induced lung injury. Through a targeted array, we identified netrin‐1 as the top upregulated neuronal guidance protein in macrophages treated with lipopolysaccharide (LPS). Furthermore, we found that netrin‐1 is highly enriched in infiltrating myeloid cells, particularly in macrophages during LPS‐induced lung injury. Transcriptional studies implicate hypoxia‐inducible factor HIF‐1α in the transcriptional induction of netrin‐1 during LPS treatment. Subsequently, the deletion of netrin‐1 in the myeloid compartment (Ntn1loxp/loxp LysM Cre) resulted in exaggerated mortality and lung inflammation. Surprisingly, further studies revealed enhanced natural killer cells (NK cells) infiltration in Ntn1loxp/loxp LysM Cre mice, and neutralization of NK cell chemoattractant chemokine (C‐C motif) ligand 2 (CCL2) reversed the exaggerated lung inflammation. Together, these studies provide functional insight into myeloid cell‐derived netrin‐1 in controlling lung inflammation through the modulation of CCL2‐dependent infiltration of NK cells.
Proteomic/transcriptomic analysis of erythropoiesis
Authors: Brand Marjorie , Ranish Jeffrey A.
Published: March 2021

Purpose of review

Erythropoiesis is a hierarchical process by which hematopoietic stem cells give rise to red blood cells through gradual cell fate restriction and maturation. Deciphering this process requires the establishment of dynamic gene regulatory networks (GRNs) that predict the response of hematopoietic cells to signals from the environment. Although GRNs have historically been derived from transcriptomic data, recent proteomic studies have revealed a major role for posttranscriptional mechanisms in regulating gene expression during erythropoiesis. These new findings highlight the need to integrate proteomic data into GRNs for a refined understanding of erythropoiesis.

Recent findings

Here, we review recent proteomic studies that have furthered our understanding of erythropoiesis with a focus on quantitative mass spectrometry approaches to measure the abundance of transcription factors and cofactors during differentiation. Furthermore, we highlight challenges that remain in integrating transcriptomic, proteomic, and other omics data into a predictive model of erythropoiesis, and discuss the future prospect of single-cell proteomics.

Recent proteomic studies have considerably expanded our knowledge of erythropoiesis beyond the traditional transcriptomic-centric perspective. These findings have both opened up new avenues of research to increase our understanding of erythroid differentiation, while at the same time presenting new challenges in integrating multiple layers of information into a comprehensive gene regulatory model.
An Innovative antibody-based Plug-and-Play strategy for SARS-CoV-2
Authors: Shivange Gururaj , Gogoi Debananda , Tushir-Singh Jogender
Published: March 2021

The novel and highly pathogenic coronavirus (SARS-CoV-2) remains a public health threat worldwide. SARS-CoV-2 enters human host lung cells via its spike protein binding to angiotensin-converting enzyme 2 (ACE2) in a process critical dependent on host protease-mediated fusion event. Thus, effective targeted therapies blocking the first step of viral fusion and cellular entry remains a critical unmet medical need to overcome disease pathology. Here we engineered and describe an antibody-based novel and targeted plug-and-play strategy, which directly competes with the proteolytic activation function of SAR-CoV-2 spike protein. The described strategy involves the engineering of furin substrate residues in IgG1 Fc-extended flexible region of spike targeting antibody. Our results with spike receptor-binding domain (RBD) targeting CR3022 antibody support blockade of the viral function using proof of concept ACE2 overexpressing cells. Our study reveals analytical, safe, and selective mechanistic insights for SARS-CoV-2 therapeutic design and is broadly applicable to the future coronaviridae family members (including mutant variants) exploiting the host protease system for cellular entry.
Human AdV-20-42-42, a promising novel adenoviral vector for gene therapy and vaccine product development
Authors: Ballmann Mónika Z. , Raus Svjetlana , Engelhart Ruben , Kaján Győző L. , van der Zalm Chantal , Papp Tibor , John Lijo , Khan Selina , Custers Jerome , Bakker Wilfried A.M. , van der Schaar Hilde M. , Arnberg Niklas , Lemckert Angelique A.C. , Havenga Menzo , Baker Andrew H.
Published: March 2021

Pre-existing immune responses towards adenoviral vector limit the use of a vector based on particular serotypes and its clinical applicability for gene therapy and/or vaccination. Therefore, there is a significant interest to vectorize novel adenoviral types that have low seroprevalence in the human population. Here, we describe the discovery and vectorization of a chimeric human adenovirus, which we call HAdV-20-42-42. Full genome sequencing revealed that this virus is closely related to human serotype 42, except for the penton-base which is derived from serotype 20. The HAdV-20-42-42 vector could be propagated stably to high titers on existing E1-complementing packaging cell lines. Receptor binding studies revealed that the vector utilized both CAR and CD46 as receptors for cell entry. Furthermore, the HAdV-20-42-42 vector was potent in transducing human and murine cardiovascular cells and tissues, irrespective of the presence of blood coagulation factor X. In addition, the vector did not sequester in the liver upon intravenous administration in rodents. Finally, we demonstrate that potent T-cell responses against vector-delivered antigens could be induced upon vaccination. In summary, from the data obtained we conclude that HAdV-20-42-42 provides a valuable addition to the portfolio of adenoviral vectors available to develop safe and efficacious products in the fields of gene therapy and vaccination.

IMPORTANCE

Adenoviral vectors are currently under investigation for a broad range of therapeutic indications in diverse fields, such as oncology and gene therapy, as well as for vaccination both for human and veterinary use. A wealth of data shows that pre-existing immune responses may limit the use of a vector. Particularly in the current climate of global pandemic, there is a need to expand the toolbox with novel adenoviral vectors for vaccine development. Our data demonstrates that we have successfully vectorized a novel adenovirus serotype with low seroprevalence. The cell transduction data and antigen-specific immune responses inducedin vivodemonstrate that this vector is highly promising for the development of gene therapy and vaccine products.
VCFcontam: A Machine Learning Approach to Estimate Cross-Sample Contamination from Variant Call Data
Authors: McCartney-Melstad Evan , Bi Ke , Han James , Foo Catherine K.
Published: March 2021

The quality of genotyping calls resulting from DNA sequencing is reliant on high quality starting genetic material. One factor that can reduce sample quality and lead to misleading genotyping results is genetic contamination of a sample by another source, such as cells or DNA from another sample of the same or different species. Cross-sample contamination by individuals of the same species is particularly difficult to detect in DNA sequencing data, because the contaminating sequence reads look very similar to those of the intended base sample. We introduce a new method that uses a support vector regression model trained onin silicocontaminated datasets to predict empirical contamination using a collection of variables drawn from VCF files, including the fraction of sites that are heterozygous, the fraction of heterozygous sites with imbalanced allele counts, and parameters describing distributions fit to heterozygous allele fractions in a sample. We use the method described here to train a model that can accurately predict the extent of cross-sample contamination within 1% of the actual fraction, for simulated contaminated samples in the 0-5% contamination range, directly from the VCF file.

Definitions

Lesser allele

The allele in a heterozygous position that received less sequencing read support (which may be either the REF or ALT allele).

Lesser allele fraction (LAF)

The number of sequencing reads supporting the less frequently observed allele divided by the sum of reads supporting both alleles in the genotype at a given genomic position.
The neural code for face memory
Authors: She Liang , Benna Marcus K. , Shi Yuelin , Fusi Stefano , Tsao Doris Y.
Published: March 2021

The ability to recognize familiar visual objects is critical to survival. A central assumption of neuroscience is that long-term memories are represented by the same brain areas that encode sensory stimuli (1). Neurons in inferotemporal (IT) cortex represent the sensory percept of visual objects using a distributed axis code (2–4). Whether and how the same IT neural population represents the long-term memory of visual objects remains unclear. Here, we examined how familiar faces are encoded in face patch AM and perirhinal cortex. We found that familiar faces were represented in a distinct subspace from unfamiliar faces. The familiar face subspace was shifted relative to the unfamiliar face subspace at short latency and then distorted to increase neural distances between familiar faces at long latency. This distortion enabled markedly improved discrimination of familiar faces in both AM and PR. Inactivation of PR did not affect these memory traces in AM, suggesting that the memory traces arise from intrinsic recurrent processes within IT cortex or interactions with downstream regions outside the medial temporal lobe (5, 6). Overall, our results reveal that memories of familiar faces are represented in IT and perirhinal cortex by a distinct long-latency code that is optimized to distinguish familiar identities.
Deep learning from multiple experts improves identification of amyloid neuropathologies
Authors: Wong Daniel R. , Tang Ziqi , Mew Nicholas C. , Das Sakshi , Athey Justin , McAleese Kirsty E. , Kofler Julia K. , Flanagan Margaret E. , Borys Ewa , White Charles L. , Butte Atul J. , Dugger Brittany N. , Keiser Michael J.
Published: March 2021

Pathologists can label pathologies differently, making it challenging to yield consistent assessments in the absence of one ground truth. To address this problem, we present a DL approach that draws on a cohort of experts, weighs each contribution, and is robust to noisy labels. We collected 100,495 annotations on 20,099 candidate amyloid beta neuropathologies (cerebral amyloid angiopathy (CAA), and cored and diffuse plaques) from three institutions, independently annotated by five experts. DL methods trained on a consensus-of-two strategy yielded 12.6-26% improvements by area under the precision recall curve (AUPRC) when compared to those that learned individualized annotations. This strategy surpassed individual-expert models, even when unfairly assessed on benchmarks favoring them. Moreover, ensembling over individual models was robust to hidden random annotators. In blind prospective tests of 52,555 subsequent expert-annotated images, the models labeled pathologies like their human counterparts (consensus model AUPRC=0.74 cored; 0.69 CAA). This study demonstrates a means to combine multiple ground truths into a common-ground DL model that yields consistent diagnoses informed by multiple and potentially variable expert opinion.
Wrack enhancement of post-hurricane vegetation and geomorphological recovery in a coastal dune
Authors: Joyce Matthew A. , Crotty Sinead M. , Angelini Christine , Cordero Orlando , Ortals Collin , de Battisti Davide , Griffin John N
Published: March 2021

Coastal ecosystems such as sand dunes, mangrove forests, and salt marshes provide natural storm protection for vulnerable shorelines. At the same time, storms erode and redistribute biological materials among coastal systems via wrack. Yet how such cross-ecosystem subsidies affect post-storm recovery is not well understood. Here, we report an experimental investigation into the effect of storm wrack on eco-geomorphological recovery of a coastal embryo dune in north-eastern Florida, USA, following hurricane Irma. We contrasted replicated 100-m2wrack-removal and unmanipulated (control) plots, measuring vegetation and geomorphological responses over 21 months. Relative to controls, grass cover was reduced 4-fold where diverse storm wrack, including seagrass rhizomes, seaweed, and wood, was removed. Wrack removal was also associated with a reduction in mean elevation, which persisted until the end of the experiment when removal plots had a 14% lower mean elevation compared to control plots. These results suggest that subsides of wrack re-distributed from other ecosystem types (e.g. seagrasses, macroalgae, uplands): i) enhances the growth of certain dune-building grasses; and ii) boosts the geomorphological recovery of coastal dunes. Our study also indicates that the practice of post-storm beach cleaning to remove wrack – a practice widespread outside of protected areas – may undermine the resilience of coastal dunes and their services.