bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling DNA Ligase Substrate Specificity with a Pacific Biosciences Single‐Molecule Real‐Time Sequencing Assay
Authors: Duckworth Alexander T. , Bilotti Katharina , Potapov Vladimir , Lohman Gregory J. S. 
Published: March 2023

AbstractDNA ligases catalyze the joining of breaks in nucleic acid backbones and are essential enzymes for in vivo genome replication and repair across all domains of life. These enzymes are also critically important to in vitro manipulation of DNA in applications such as cloning, sequencing, and molecular diagnostics. DNA ligases generally catalyze the formation of a phosphodiester bond between an adjacent 5′‐phosphate and 3′‐hydroxyl in DNA, but they exhibit different substrate structure preferences, sequence‐dependent biases in reaction kinetics, and variable tolerance for mismatched base pairs. Information on substrate structure and sequence specificity can inform both biological roles and molecular biology applications of these enzymes. Given the high complexity of DNA sequence space, testing DNA ligase substrate specificity on individual nucleic acid sequences in parallel rapidly becomes impractical when a large sequence space is investigated. Here, we describe methods for investigating DNA ligase sequence bias and mismatch discrimination using Pacific Biosciences Single‐Molecule Real‐Time (PacBio SMRT) sequencing technology. Through its rolling‐circle amplification methodology, SMRT sequencing can give multiple reads of the same insert. This feature permits high‐quality top‐ and bottom‐strand consensus sequences to be determined while preserving information on top‐bottom strand mismatches that can be obfuscated or lost when using other sequencing methods. Thus, PacBio SMRT sequencing is uniquely suited to measuring substrate bias and enzyme fidelity through multiplexing a diverse set of sequences in a single reaction. The protocols describe substrate synthesis, library preparation, and data analysis methods suitable for measuring fidelity and bias of DNA ligases. The methods are easily adapted to different nucleic acid substrate structures and can be used to characterize many enzymes under a variety of reaction conditions and sequence contexts in a rapid and high‐throughput manner. © 2023 New England Biolabs and The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Preparation of overhang DNA substrates for ligationBasic Protocol 2: Preparation of ligation fidelity librariesSupport Protocol 1: Preparation of ligation libraries for PacBio Sequel II sequencingSupport Protocol 2: Loading and sequencing of a prepared library on the Sequel II instrumentBasic Protocol 3: Computational processing of ligase fidelity sequencing data
p16INK4A flow cytometry of exfoliated cervical cells: Its role in quantitative pathology and clinical diagnosis of squamous intraepithelial lesions
Authors: He Yifeng , Shi Jun , Zhao Hui , Wang Yuefei , Zhang Chi , Han Sai , He Qizhi , Li Xiaolan , Li Shangji , Wang Wenjing , Yi Muhua , Hu Xiaoling , Xing Zhihua , Han Hao , Gao Yinshuang , Zhou Qing , Lu Linlin , Guo Jianfen , Cao Hui , Lu Caiping , Hou Yanqiang , Chen Dan , Yang Fengyun , Lei Ping , Di Wen , Qian Ji , Xia Yi , Zhang Youzhong , Deng Yang , Zhu Jianlong , Xu Congjian 
Published: March 2023

AbstractBackgroundP16INK4A is a surrogate signature compensating for the specificity and/or sensitivity deficiencies of the human papillomavirus (HPV) DNA and Papanicolaou smear (Pap) co‐test for detecting high‐grade cervical squamous intraepithelial lesions or worse (HSIL+). However, traditional p16INK4A immunostaining is labour intensive and skill demanding, and subjective biases cannot be avoided. Herein, we created a high‐throughput, quantitative diagnostic device, p16INK4A flow cytometry (FCM) and assessed its performances in cervical cancer screening and prevention.MethodsP16INK4A FCM was built upon a novel antibody clone and a series of positive and negative (p16INK4A‐knockout) standards. Since 2018, 24 100‐women (HPV‐positive/‐negative, Pap‐normal/‐abnormal) have been enrolled nationwide for two‐tier validation work. In cross‐sectional studies, age‐ and viral genotype‐dependent expression of p16INK4A was investigated, and optimal diagnostic parameter cut‐offs (using colposcopy and biopsy as a gold standard) were obtained. In cohort studies, the 2‐year prognostic values of p16INK4A were investigated with other risk factors by multivariate regression analyses in three cervicopathological conditions: HPV‐positive Pap‐normal, Pap‐abnormal biopsy‐negative and biopsy‐confirmed LSIL.ResultsP16INK4A FCM detected a minimal ratio of 0.01% positive cells. The p16INK4A‐positive ratio was 13.9 ± 1.8% among HPV‐negative NILM women and peaked at the ages of 40–49 years; after HPV infection, the ratio increased to 15.1 ± 1.6%, varying with the carcinogenesis of the viral genotype. Further increments were found in women with neoplastic lesions (HPV‐negative: 17.7 ± 5.0–21.4 ± 7.2%; HPV‐positive: 18.0 ± 5.2–20.0 ± 9.9%). Extremely low expression of p16INK4A was observed in women with HSILs. As the HPV‐combined double‐cut‐off‐ratio criterion was adopted, a Youden's index of 0.78 was obtained, which was significantly higher than that (0.72) of the HPV and Pap co‐test. The p16INK4A‐abnormal situation was an independent HSIL+ risk factor for 2‐year outcomes in all three cervicopathological conditions investigated (hazard ratios: 4.3–7.2).ConclusionsFCM‐based p16INK4A quantification offers a better choice for conveniently and precisely monitoring the occurrence of HSIL+ and directing risk‐stratification‐based interventions.
Synergistic use of UAV surveys, satellite tracking data, and mark‐recapture to estimate abundance of elusive species
Authors: Stokes Holly J. , Mortimer Jeanne A. , Laloë Jacques‐Olivier , Hays Graeme C. , Esteban Nicole 
Published: March 2023

AbstractEstimating population abundance is central to many ecological studies and important in conservation planning. Yet the elusive nature of many species makes estimating their abundance challenging. Abundance estimates of sea turtles, marine birds, and seals are usually made when breeding adults are ashore, while life stages spent at sea, including as juveniles, are often poorly sampled. We used a combination of high‐resolution satellite tracking (Fastloc‐GPS), uncrewed aerial vehicle (UAV) surveys, and capture‐mark‐recapture approaches to assess the abundance of immature hawksbill (Eretmochelys imbricata) and green turtles (Chelonia mydas) in a tidal lagoon of the Chagos Archipelago (Indian Ocean). We captured, marked, and released 50 turtles (48 hawksbill and 2 green turtles) prior to UAV surveys and used satellite tracking data from 27 immature turtles (25 hawksbill and 2 green turtles) to refine the estimated numbers of marked turtles available for resighting and those likely to have emigrated from the study area. We estimated a total of 339 turtles in the lagoon with a density variation at different tidal heights between 265 turtles km−2 at high water and 499 turtles km−2 at low water. Of these, 91% were hawksbills and 9% were green turtles. These hawksbill densities are the highest reported among 17 foraging sites recorded around the world and likely reflect successful long‐term protection of turtles in the Chagos Archipelago.
Heritability of plastic trait changes in drought‐exposed ponderosa pine seedlings
Authors: Wu Dean , Shu Mengjun , Moran Emily V. 
Published: March 2023

AbstractClimate change is imposing new selective pressures on forest tree populations. Evolutionary responses may be important for trees, despite long generation times, since many populations harbor significant genetic variation in environmentally relevant traits. However, the heritability of climate responses (e.g., how much growth differs under drought) has been investigated in only one tree species previously. Here, we quantify heritable variation in environmental response traits of Pinus ponderosa using a greenhouse trial. Five seedlings from each maternal family were exposed to either wet or dry treatments for four months. Traits measured include height and root length, root:shoot mass ratios, and stomatal density and number of rows. Narrow‐sense heritability for all traits was estimated using a half‐sib analysis. Many traits varied by treatment, and some also differed along gradients of “home” climate. Dry treatment root‐to‐shoot dry mass ratio was associated with survival in that treatment. Estimated heritability for drought responsiveness ranged from 0.15 to 0.65, with the highest values occurring in height growth responses. Variation was particularly high for shoot growth under drought conditions. Our results suggest that increasingly arid conditions could result in strong responses to selection.
Synthesis and Structural Characterization of Divalent Transition Metal Alkynylamidinate Complexes
Authors: Wang Sida , Liebing Phil , Feneberg Martin , Sroor Farid M. , Engelhardt Felix , Hilfert Liane , Busse Sabine , Kluth Elias , Goldhahn Rüdiger , Edelmann Frank T. 
Published: March 2023

AbstractA series of new alkynylamidinate complexes of selected first and second row transition metals has been synthesized and fully characterized. Treatment of MCl2 precursors (M=Mn, Fe, Co) with 2 equiv. of the lithium alkynylamidinates Li[c‐C3H5−C≡C−C(NR′)2] ⋅ THF (R′=iPr (2), Cy (cyclohexyl) (2)) afforded a series of binuclear complexes of the type M2[c‐C3H5−C≡C−C(NR)2‐κN:κN′]2[c‐C3H5−C≡C−C(NR)2‐κ2N,N′]2 (3: M=Mn, R=Cy; 4 a: M=Fe, R=iPr; 4 b: M=Fe, R=Cy; 5: M=Co, R=iPr) with no significant metal‐metal bonding. In marked contrast, a similar reaction of CrCl2 with 2 equiv. of 1 afforded the homoleptic dinuclear chromium(II) complex Cr2[c‐C3H5−C≡C−C(NiPr)2‐κN:κN′]4 (6) which supposedly comprises a Cr−Cr quadruple bond. Complex 6 could also be prepared in a more rational way and in better yield (61 %) by using dichromium(II) tetraacetate, Cr2(OAc)4, as starting material. Related reactions employing dimolybdenum(II) tetraacetate, Mo2(OAc)4, and 2 or 3 equiv. of 1 afforded the mixed‐ligand paddle wheel‐type complexes trans‐Mo2(OAc‐κO:κO′)2([c‐C3H5−C≡C−C(NiPr)2‐κN:κN′]2 (7) and Mo2(OAc‐κO:κO′)([c‐C3H5−C≡C−C(NiPr)2‐κN:κN′]3 (8). All title compounds were structurally characterized through single‐crystal X‐ray diffraction and spectroscopic techniques (NMR, IR, Raman).
Reconfigurability analysis of an all‐dielectric thermal microfluidic‐based metasurface
Authors: AlGhamdi Ahmed , Yousaf Jawad , Yahyaoui Ali , Sobahi Nebras , Hakim Bandar , Mittra Raj , Rmili Hatem 
Published: March 2023

AbstractMetasurface tuning is performed using different ways for a wide range of applications. This study presents the design of a thermally‐tuned all‐dielectric reconfigurable metasurface. A microfluidic channel, filled with different concentrations of tellurium–selenium (Te‐Se) alloy, is added on the top of the elliptical dielectric resonator (EDR) unit cell of the considered metasurface. The electrical properties of used semiconductor alloy are varied in the range of 400 to 700°C (steps size of 100°C). The impact of thermal tuning on the reflection and transmission characteristics of the designed metasurface is analyzed in the frequency range of 20–30 GHz using COMSOL Multiphysics. Obtained results demonstrated that the realized metasurface exhibits reconfigurable behavior in terms of variations in the reflection and transmission characteristics with a change in either temperature or concentrations of selenium and tellurium. The wider bands with high reflection and low transmission frequency bands are obtained with lower concentrations of selenium and tellurium for all operating temperatures.
Food, gut barrier dysfunction, and related diseases: A new target for future individualized disease prevention and management
Authors: Liang Linda , Saunders Clarissa , Sanossian Nerses 
Published: March 2023

AbstractDysfunction of gut barrier is known as “leaky gut” or increased intestinal permeability. Numerous recent scientific evidences showed the association between gut dysfunction and multiple gastrointestinal tract (GI) and non‐GI diseases. Research also demonstrated that food plays a crucial role to cause or remedy gut dysfunction related to diseases. We reviewed recent articles from electronic databases, mainly PubMed. The data were based on animal models, cell models, and human research in vivo and in vitro models. In this comprehensive review, our aim focused on the relationship between dietary factors, intestinal permeability dysfunction, and related diseases. This review synthesizes currently available literature and is discussed in three parts: (a) the mechanism of gut barrier and function, (b) food and dietary supplements that may promote gut health, and food or medication that may alter gut function, and (c) a table that organizes the synthesized information by general mechanisms for diseases related to leaky gut/intestinal permeability and associated dietary influences. With future research, dietary intervention could be a new target for individualized disease prevention and management.
Biomarkers of gut barrier dysfunction and risk of hepatocellular carcinoma in the REVEAL‐HBV and REVEAL‐HCV cohort studies
Authors: Petrick Jessica L. , Florio Andrea A. , Zen Jane , Wang Yanyu , Gewirtz Andrew T. , Pfeiffer Ruth M. , Loftus Sarah , Inglefield Jon , Koshiol Jill , Yang Baiyu , Yu Kelly , Hildesheim Allan , Chen Chien‐Jen , Yang Hwai‐I , Lee Mei‐Hsuan , McGlynn Katherine A. 
Published: March 2023

AbstractGut barrier dysfunction can result in the liver being exposed to an elevated level of gut‐derived bacterial products via portal circulation. Growing evidence suggests that systemic exposure to these bacterial products promotes liver diseases including hepatitis, cirrhosis, and hepatocellular carcinoma (HCC). However, prospective studies have not examined the association between biomarkers of gut barrier dysfunction and HCC risk in a population of hepatitis B or C viral (HBV/HCV) carriers. We investigated whether prediagnostic, circulating biomarkers of gut barrier dysfunction were associated with HCC risk, using the Risk Evaluation of Viral Load Elevation and Associated Liver Disease/Cancer (REVEAL)‐HBV and REVEAL‐HCV cohorts from Taiwan. REVEAL‐HBV included 185 cases and 161 matched controls, and REVEAL‐HCV 96 cases and 96 matched controls. The biomarkers quantitated were immunoglobulin A (IgA), IgG, and IgM against lipopolysaccharide (LPS) and flagellin, soluble CD14 (an LPS coreceptor), and LPS‐binding protein (LBP). Odds ratios (ORs) and 95% confidence intervals (CIs) for associations between biomarker levels and HCC were calculated using multivariable‐adjusted logistic regression. A doubling of the circulating levels of antiflagellin IgA or LBP was associated with a 76% to 93% increased risk of HBV‐related HCC (OR per one unit change in log2 antiflagellin IgA = 1.76, 95% CI: 1.06‐2.93; OR for LBP = 1.93, 95% CI: 1.10‐3.38). None of the other markers were associated with an increased risk of HBV‐related or HCV‐related HCC. Results were similar when cases diagnosed in the first 5 years of follow‐up were excluded. Our findings contribute to understanding the interplay of gut barrier dysfunction and primary liver cancer etiology.
Activity and steady‐state kinetics of one‐dimensional kinetic Ising model
Authors: Liang Kuo Kan 
Published: March 2023

AbstractIn this work, we focused on the kinetics of a one‐dimensional Ising system (1DIS) with constant nearest‐neighbor interaction (NNI). The exact solution of both thermodynamics and kinetics of this system under quasi‐chemical approximation (QCA) had been shown in the literature, and the equilibrium solution was exact. In this work, it was discussed why QCA applied the best in the case of 1DIS with constant NNI. Furthermore, extension had been made to discuss that due to this special reason, perhaps the kinetics of the system under QCA is the correct steady‐state kinetics. Inspired by this observation, the activity and activity coefficients of the system was studied closely to re‐examine the form of the equation of motion under QCA. A novel concept—the instantaneous activities and the corresponding instantaneous activity coefficients—was introduced, and in terms of these quantities the kinetics seemed to be much simpler and physically more meaningful. The chevron plot of this system was also discussed and new way of looking at the rollover of chevron plots was presented.
Supramolecular assembly and solvochromic luminescence of a Au(I) complex containing di(4‐pyridylmethyl)aminedithiocarbamate
Authors: Tzeng Biing‐Chiau , Hung Jun‐Wei , Wu Chung‐Lun , Lee Gene‐Hsiang 
Published: March 2023

AbstractThe di(4‐pyridylmethyl)aminedithiocarbamate (DPMACS2) ligand was used to react with (Me2S)AuCl to give a dinuclear complex, [Au(DPMACS2)]2, which shows both intramolecular Au(I)⋅⋅⋅Au(I) distances of 2.741(9)–2.788(1) Å and intermolecular Au(I)···Au(I) contacts of 2.917(5)–3.047(7) Å, leading to 1‐D Au(I) chains in the solid state. In addition, complex [Au(DPMACS2)]2 shows the luminescence at 555 nm at room temperature while excited, and almost no energy shift for the luminescence at 553 nm upon grinding has been observed. In this regard, we further examined the solvochromic luminescence upon grinding with various solvents, and the luminescence is within 549–572 nm. It is noted that the solvochromic luminescence for dichloromethane (566 nm) and 1,2‐dichloroethane (572 nm) has been observed, and the original luminescence at 555 nm can be restored upon solvent loss. Indeed, such red‐shifts for the solvochromic luminescence are most likely due to a decrease in intermolecular Au(I)⋅⋅⋅Au(I) contacts while solvents entering into crystal lattices upon grinding and it is a reversible process upon solvent loss.
T‐cell exhaustion: A potential target biomarker of the tumour microenvironment affecting oesophageal adenocarcinoma
Authors: Peng Shiyu , Han Xiaojiang , Geng Wenbin , Zhao Lifang 
Published: March 2023

AbstractBackgroundOesophageal adenocarcinoma (EAC) is one of the most common malignant tumours, and the number of patients is increasing year by year. T‐cell exhaustion (TEX) is an important risk factor for tumour immunosuppression and invasion, but its underlying mechanism in the pathogenesis of EAC is not clear.MethodsUnsupervised clustering was performed to screen relevant genes based on Gene Set Variation Analysis scores of the three pathways of the HALLMARK gene set IL2/IFNG/TNFA. Multiple enrichment analyses and data combinations were used to depict the relationship between TEX‐related risk models and CIBERSORTx immune infiltrating cells. In addition, to explore the impact of TEX on EAC therapeutic resistance, we assessed the impact of TEX risk models on the therapeutic sensitivity of various novel drugs using single‐cell sequencing and searched for their potential therapeutic targets and cellular communication.ResultsFour risk clusters of EAC patients were identified by unsupervised clustering and searched for potential TEX‐related genes. Based on this, LASSO regression and decision trees were used to construct risk prognostic models containing a total of three TEX‐associated genes in EAC. The results showed that TEX risk scores were significantly associated with the survival prognosis of EAC patients in both the Cancer Genome Atlas dataset and the independent validation set of Gene Expression Omnibus. Immune infiltration and cell communication analyses identified mast cell resting as a protective factor in TEX, and pathway enrichment analyses showed that the TEX risk model was highly associated with multiple chemokines as well as inflammation‐associated pathways. In addition, higher TEX risk scores were associated with a weak responsiveness to immunotherapy.ConclusionWe describe the immune infiltration, prognostic significance and potential possible mechanisms of TEX in the EAC patient population. This is a novel attempt to promote the development of novel therapeutic modalities and immunological target construction for oesophageal adenocarcinoma. It is expected to make a potential contribution to advancing the exploration of immunological mechanisms and the opening of target drugs in EAC.
Competitive, multi‐objective, and compartmented Flux Balance Analysis for addressing tissue‐specific inborn errors of metabolism
Authors: Liu Yanhua , Westerhoff Hans V. 
Published: March 2023

AbstractThe inborn error of metabolism phenylketonuria (PKU, OMIM 261600) is most often due to inactivation of phenylalanine hydroxylase (PAH), which converts phenylalanine (Phe) into tyrosine (Tyr). The reduced PAH activity increases blood concentration of phenylalanine and urine levels of phenylpyruvate. Flux balance analysis (FBA) of a single‐compartment model of PKU predicts that maximum growth rate should be reduced unless Tyr is supplemented. However, the PKU phenotype is lack of development of brain function specifically, and Phe reduction rather than Tyr supplementation cures the disease. Phe and Tyr cross the blood–brain barrier (BBB) through the aromatic amino acid transporter implying that the two transport reactions interact. However, FBA does not accommodate such competitive interactions. We here report on an extension to FBA that enables it to deal with such interactions. We built a three‐compartment model, made the common transport across the BBB explicit, and included dopamine and serotonin synthesis as parts of the brain function to be delivered by FBA. With these ramifications, FBA of the genome‐scale metabolic model extended to three compartments does explain that (i) the disease is brain specific, (ii) phenylpyruvate in urine is a biomarker, (iii) excess of blood‐phenylalanine rather than shortage of blood‐tyrosine causes brain pathology, and (iv) Phe deprivation is the better therapy. The new approach also suggests (v) explanations for differences in pathology between individuals with the same PAH inactivation, and (vi) interference of disease and therapy with the functioning of other neurotransmitters.
Reduced neutralizing antibody response to SARS‐CoV‐2 vaccine booster dose in people living with HIV with severe immunosuppression
Authors: Corma‐Gómez Anaïs , Fernández‐Fuertes Marta , Viñuela Laura , Domínguez Carmen , Santos Marta , Fuentes‐López Ana , Rojas Almudena , Fernández‐Pérez Nieves , Martín‐Carmona Jessica , Serrano‐Conde Esther , Real Luis M. , Mendoza Joaquín , Macías Juan , Pineda Juan A. , García Federico 
Published: March 2023

AbstractThe aim of this study was to assess the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) vaccines among people living with HIV (PLWH) with severe immunosuppression, after a booster dose. The design was a case–control study nested in a prospective cohort of PLWH. All patients with CD4 cell count <200 cells/mm3 who had received additional dose of messenger RNA (mRNA) COVID‐19 vaccine, after a standard immunization scheme were included. Control group: patients age‐ and sex‐matched, with CD4 ≥ 200 cells/mm3, in the ratio of 2:1. Antibody response to a booster dose (anti‐S levels 33.8 ≥ BAU/mL) and neutralizing activity against SARS‐CoV‐2 B.1, B.1.617.2, and Omicron BA.1, BA.2, and BA.5 strains were assessed after the booster shot. Fifty‐four PLWH were included, 18 with CD4 counts < 200 cells/mm3. Fifty‐one (94%) showed response to a booster dose. Response was less frequent in PLWH with CD4 < 200 cells/mm3 than in those with CD4 counts ≥ 200 cells/mm3 (15 [83%] vs. 36 [100%], p = 0.033). In the multivariate analysis, CD4 counts ≥ 200 cells/mm3 [incidence rate ratio (IRR) = 18.1 (95% confidence interval [CI]: 16.8–19.5), p < 0.001] was associated with a higher probability of showing antibody response. Neutralization activity against SARS‐CoV‐2 B.1, B.1.617, BA.1, and BA.2 strains was significantly inferior among individuals with CD4 counts < 200 cells/mm3. In conclusion, among PLWH with CD4 counts < 200 cells/mm3, the immune response elicited by mRNA additional vaccine dose is reduced.