bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutual socialization during shared media moments: U.S. LGBTQ teens and their parents negotiate identity support
Authors: Mares Marie-Louise , Chen Yuchi Anthony , Bond Bradley J 
Published: January 2023

AbstractSocial relational theory proposes that children and parents socialize each other, particularly when knowledge, beliefs, and identities diverge. For families with lesbian, gay, bisexual, transgender, queer (LGBTQ) teens, identity-relevant media depictions may spark moments of mutual socialization, including attempts to mediate each other’s viewing and discussions of the teen’s identity. U.S. data from 200 LGBTQ teens (aged 13–18) and one of their parents indicated that 83% of dyads reported that media content had elicited identity-related conversations. Both teens and parents perceived teens to mediate more often than parents, though latent profile analyses suggested distinct dyadic profiles. Although all teens were out to their parent, those with more identity certainty engaged in and received more frequent mediation. For parents, the frequency and positivity of “media moments” were associated with greater support for their teen’s identity. For teens, positivity (but not frequency) of such moments was associated with perceptions of more parental support for their identity.
Profiles of Resilience, Distress, and Posttraumatic Growth in Parents of Children with Cancer and the Relation to Subsequent Parenting and Family Functioning
Authors: Howard Sharp Katianne M , Tillery Webster Rachel , Cook Jessica , Okado Yuko , Long Alanna , Phipps Sean 
Published: January 2023

Abstract

Objective
The aim of this study was to identify patterns of distress and growth in parents of children with cancer and examine associations with subsequent parenting, parent–child relationship, and family environment.

Methods
Participants included children with cancer history (8–17 years) stratified by time since diagnosis and their parent. At enrollment, parents (n = 254) reported depression and anxiety, and post-traumatic stress symptoms, posttraumatic growth (PTG), and benefit finding in relation to their child’s cancer. Three years later, children (n = 214) reported parenting behavior, parent reactions to their distress, and family environment. Parents reported their reaction to children’s distress and qualities of the parent–child relationship.

Results
Latent profile analysis empirically identified 3 cross-sectional profiles using baseline data: “Resilience, High Growth” (50%), characterized by the lowest distress and the highest PTG/benefit finding; “Moderate Distress with Growth” (33%), characterized by relatively high levels of all indicators; and “Resilience, Low Growth” (17%), characterized by relatively low distress with low PTG/benefit finding. Membership in profiles was associated with parent gender; parents’ stressful life events; socioeconomic status; and child diagnosis, on versus off treatment status, and treatment intensity. Parent membership in the Moderate Distress with Growth profile was generally linked with poorer parenting behavior, parent–child relationship quality, and family functioning.

Conclusion
The majority of parents exhibited resilience and growth. However, a subset of parents displaying moderate distress may be at risk for subsequent parenting and family functioning challenges. Findings further highlight the importance of screening for even moderate parent distress and the possible impact of parent psychosocial interventions indirectly on parenting and family functioning.
Comparison of Solute Nanoclusters in Fe–Cr–N Tempered Martensite Observed by Different Atom Probe Instruments
Authors: Zhang Yong-Jie , Young Shao-Wen , Rice Katherine P , Sato Mitsutaka , Miyamoto Goro , Furuhara Tadashi , Ohkubo Tadakatsu , Hono Kazuhiro 
Published: January 2023

AbstractThe solute clustering behaviors in Fe-1.0mass%Cr-0.3mass%N tempered martensite were comparatively studied by using three atom probe instruments, i.e. LEAP 4000 HR, 5000 XR, and 5000 XS. The microstructural features of nanoclusters were measured under the same conditions in voltage pulse mode, while statistical analysis including nearest neighbor distribution, radial distribution, frequency distribution, and cluster size distribution of Cr atoms were performed on the reconstructed datasets. The results revealed the superior capability of the LEAP 5000 XR to detect Cr nanoclusters in tempered martensite compared with the LEAP 4000 HR as a result of the improvement in detection efficiency and hit detection performance, whereas the high level of background in the mass-to-charge spectrum measured by the LEAP 5000 XS in voltage pulse mode limits its application in the detection of solute nanoclusters.
Observation of Focused Ion Beam-Induced Artifacts in Transmission Electron Microscopy Samples Leading to the Epitaxial Growth of AlGaSb Quantum Dots on the GaSb Substrate
Authors: Cummings Damion P , Perry Daniel L , Jauregui Luis Jose , Deitz Julia , Klem John F , Pan Wei , Lu Ping 
Published: January 2023

Abstract
We report an unusual artifact induced by Ga+ or Xe+ focused ion beam (FIB) preparation in transmission electron microscopy (TEM) samples with epitaxial layers on a GaSb substrate. The Ga+ FIB-ed TEM samples with a quantum structure made of Al/AlSb/GaSb/InAs/Al0.33Ga0.67Sb multilayers on a GaSb substrate are found to undergo phase modifications under certain conditions related to the beam energy. Dependent on the voltage used during thinning, the Al islands initially on top of the multilayer stack are gradually replaced by Ga, leading to the epitaxial formation of AlxGa1-xSb (AlGaSb) quantum dots (QDs) whose shapes are conformed to the initial Al islands. A similar effect is observed when the top Al islands are capped by an amorphous As layer. The artifacts can be avoided by extensive thinning at 5 kV followed by 2 kV polishing. Further experiments using Xe+ plasma FIB (PFIB) also produce similar artifacts, and those effects are eliminated by Xe+ PFIB under cryogenic conditions regardless of the beam conditions. The mechanism for forming the epitaxial AlGaSb QDs is investigated, and potential use of this phenomenon for QD fabrication is discussed.
Computer Vision Applied to In-Situ Specimen Orientation Adjustment for Quantitative SEM Analysis
Authors: Klein Clay , Li Chunfei 
Published: January 2023

Abstract
Quantitative analysis methods based on the usage of a scanning electron microscope (SEM), such as energy-dispersive X-ray spectroscopy, often require specimens to have a flat surface oriented normal to the electron beam. In-situ procedures for putting microscopic flat surfaces into this orientation generally rely on stereoscopic methods that measure the change in surface vector projections when the surface is tilted by some known angle. Although these methods have been used in the past, there is no detailed statistical analysis of the uncertainties involved in such methods, which leaves an uncertainty in how precisely a specimen can be oriented. Here, we present a first principles derivation of a specimen orientation method and apply our method to a flat sample to demonstrate it. Unlike previous works, we develop a computer vision program using the scale-invariant feature transform to automate and expedite the process of making measurements on our SEM images, thus enabling a detailed statistical analysis of the method with a large sample size. We find that our specimen orientation method is able to orient flat surfaces with high precision and can further provide insight into errors involved in the standard SEM rotation and tilt operations.
The Impact of Energy Filtering on Fluctuation Electron Microscopy
Authors: Radić Dražen , Peterlechner Martin , Posselt Matthias , Bracht Hartmut 
Published: January 2023

Abstract
Fluctuation electron microscopy (FEM) analyzes intensity fluctuations within diffraction patterns in order to draw conclusions regarding the structure of amorphous materials by calculating the normalized variance V(k,R). Ideally, such experiments only evaluate elastically diffracted electrons. However, an undesired inelastic background intensity is always present and degrades the FEM data. Energy filtered FEM experiments were performed on amorphous germanium created by self-ion implantation. FEM data were acquired in a transmission electron microscope at 60 and 300 kV with different electron doses as well as varying energy filter slit widths at two sample thicknesses. Generally, the measurements reveal that energy filtering greatly improves FEM data at both beam energies and sample thicknesses by removing a certain amount of the inelastic background intensity in the diffraction patterns. The narrower the energy filter, the larger the normalized variance. This brings energy filtered FEM data closer to the normalized variance determined by simulations under idealized conditions. Furthermore, preliminary results indicate that the medium range order length scale extracted from the pair-persistence analysis used in FEM is strongly affected by energy filtering.
Ultrastructure of the Oropharyngeal Cavity Floor of the Red Porgy (Pagrus pagrus) by Light and Scanning Electron Microscopy
Authors: Alsafy Mohamed A M , Seif Manal A , El-Gendy Samir A A , El-Beskawy Mohamed , El Dakroury Mohamed 
Published: January 2023

Abstract
The current research aim is an ultrastructural examination of the floor of the oropharyngeal cavity of the red porgy fish. The study used gross morphology, light and scanning electron microscopy, and morphometric analysis. The teeth are arranged in anterior and posterior rows with differing heights along the entire length of the lower jaw. The labial teeth were long papilliform (canine like), medium, and short papilliform teeth. The teeth had a central pulp cavity and were surrounded by a thick dentine ridge covered in enamel. The pharyngeal teeth appeared in a V-shaped structure after the end of the interbranchial septum. There were three sizes of pharyngeal teeth: long, medium, and short. The apical pouch appeared on the lateral sides of the tongue. The tongue had a bulged mountaintop in the center and lateral sides with sea-wave-like longitudinal ridges with sloping grooves between them. The whole tongue surface had longitudinal ridges and sharp transverse ridges that appeared thorn like at the tongue root. Many sizes of pointed papillae were visible along the tongue surface. Ruffini corpuscles have been discovered in the tongue’s conical and dome-shaped papillae. The red porgy’s teeth and tongue papillae have distinct structural characteristics that are reflected in their carnivorous behavior.
The Effect of Dynamical Scattering on Single-plane Phase Retrieval in Electron Ptychography
Authors: Clark Laura , Martinez Gerardo T , O’Leary Colum M , Yang Hao , Ding Zhiyuan , Petersen Timothy C , Findlay Scott D , Nellist Peter D 
Published: January 2023

Abstract
Segmented and pixelated detectors on scanning transmission electron microscopes enable the complex specimen transmission function to be reconstructed. Imaging the transmission function is key to interpreting the electric and magnetic properties of the specimen, and as such four-dimensional scanning transmission electron microscopy (4D-STEM) imaging techniques are crucial for our understanding of functional materials. Many of the algorithms used in the reconstruction of the transmission function rely on the multiplicative approximation and the (weak) phase object approximation, which are not valid for many materials, particularly at high resolution. Herein, we study the breakdown of simple phase imaging in thicker samples. We demonstrate the behavior of integrated center of mass imaging, single-side band ptychography, and Wigner distribution deconvolution over a thickness series of simulated GaN 4D-STEM datasets. We further give guidance as to the optimal focal conditions for obtaining a more interpretable dataset using these algorithms.
Bullseye Analysis: A Fluorescence Microscopy Technique to Detect Local Changes in Intracellular Reactive Oxygen Species (ROS) Production
Authors: Hughes Joshua G , Chisholm David R , Whiting Andrew , Girkin John M , Ambler Carrie A 
Published: January 2023

AbstractReactive oxygen species (ROS) are naturally produced compounds that play important roles in cell signaling, gene regulation, and biological defense, including involvement in the oxidative burst that is central to the anti-microbial actions of macrophages. However, these highly reactive, short-lived radical species also stimulate cells to undergo programmed cell death at high concentrations, as well as causing detrimental effects such as oxidation of macromolecules at more moderate levels. Imaging ROS is highly challenging, with many researchers working on the challenge over the past 10–15 years without producing a definitive method. We report a new fluorescence microscopy-based technique, Bullseye Analysis. This methodology is based on concepts provided by the FRAP (Fluorescence Recovery after Photobleaching) technique and refined to evidence the spatiotemporal production of ROS, and the subsequent consequences, on a subcellular scale. To exemplify the technique, we have used the ROS-reporter dye, CellROX, and the ROS-inducing photosensitizer, LightOx58, a potent source of ROS compared with UV irradiation alone. Further validation of the technique was carried out using differing co-stains, notably Mitotracker and JC-1.
Metathoracic Glands ofScaptocoris castaneaPerty, 1833 (Heteroptera: Cydnidae): Morphology and Volatilomic
Authors: Cossolin Jamile Fernanda Silva , Martínez Luis Carlos , Pereira Mônica Josene Barbosa , Vivan Lucia Madalena , dos Santos Marcelo Henrique , Fiaz Muhammad , Carvalho Paulo Eduardo Gomes Rodrigues , Souza Camila Patrícia Ribeiro , Serrão José Eduardo 
Published: January 2023

AbstractThe characteristic odor of Heteroptera is produced by metathoracic glands, which is poorly evaluated in the brown stink bug Scaptocoris castanea Perty, 1833 (Heteroptera: Cydnidae), an important agricultural pest. This study describes the anatomy, histology, and ultrastructure of the external scent efferent system, associated metathoracic gland, and volatile compounds produced. The external scent efferent system of S. castanea is ventrally located in the thorax, with an ovoid ostiole, a small and protruded peritreme, and an evaporatory area (evaporatorium) rich in mycoid microsculptures. The metathoracic glands have a secretory region with irregular tubules that open into a large reservoir. The secretory epithelium of the metathoracic gland has bicellular secretory units with globular and canaliculus cells. The globular cells are rich in rough endoplasmic reticulum, mitochondria, and secretory vesicles. The reservoir has a single layered cubic epithelium with apical surface lined by a thin cuticular intima, and cytoplasm rich in mitochondria, lysosomes, and secretory vesicles. The secretion of the metathoracic glands of S. castanea has 11 components, including aldehydes, alcohols, and hydrocarbons, with abundant (E)-2-decenal, 2-octenal, 2-hexenal, and 1-octen-3-yl acetate. This study fills an important gap in understanding defensive strategy in this agricultural pest.
Distribution and Ultrastructural Features of Telocytes in the Pars Distalis of the Rat Pituitary Gland
Authors: Chunhua Liang , Xuebing Bai , Yonghong Shi , Min Yang , Haixiang Huang , Jianming Yue , Zhenwei Zhang , Qiusheng Chen 
Published: January 2023

AbstractTelocytes (TCs), a novel type of interstitial cells, are characterized by their smaller cellular body and extremely long, thin processes which are called telopodes (Tps). They have been described in multiple organs from diverse animals. Currently, the existence of TCs in rat pars distalis (PD) has remained unexplored. This investigation was undertaken to visualize the distribution and structural features of TCs in the PD using immunofluorescence (IF) and further validated by transmission electron microscopy (TEM). HE staining revealed the presence of interstitial cells in the peri-sinusoidal vessels spaces of the PD. Using IF, CD34/vimentin double-positive interstitial cells were identified as TCs in accordance with identification standards. TEM further verified the presence of TCs based on their unique ultrastructural features. TCs exhibited communication structures including cell connections and extracellular vesicles (EVs). Interestingly, TCs were in close proximity to the nerves. Most importantly, Tps extended toward the nerves, blood vessels, and glandular cells. TCs could be the structural foundation of a third regulatory system in rat PD according to the tight connections of TCs with sinusoid vessels, glandular cells, EVs and most crucially the nerves. Taken together, these morphological and structural findings demonstrate that TCs are vital components of the rat PD.
Faster SARS-CoV-2 sequence validation and annotation for GenBank using VADR
Authors: Nawrocki Eric P 
Published: January 2023

Abstract
In 2020 and 2021, &gt;1.5 million SARS-CoV-2 sequences were submitted to GenBank. The initial version (v1.0) of the VADR (Viral Annotation DefineR) software package that GenBank uses to automatically validate and annotate incoming viral sequences is too slow and memory intensive to process many thousands of SARS-CoV-2 sequences in a reasonable amount of time. Additionally, long stretches of ambiguous N nucleotides, which are common in many SARS-CoV-2 sequences, prevent VADR from accurate validation and annotation. VADR has been updated to more accurately and rapidly annotate SARS-CoV-2 sequences. Stretches of consecutive Ns are now identified and temporarily replaced with expected nucleotides to facilitate processing, and the slowest steps have been overhauled using blastn and glsearch, increasing speed, reducing the memory requirement from 64Gb to 2Gb per thread, and allowing simple, coarse-grained parallelization on multiple processors per host. VADR is now nearly 1000 times faster than it was in early 2020 SARS-CoV-2 sequence processing. It has been used to screen and annotate more than 1.5 million SARS-CoV-2 sequences since June 2020, and it is now efficient enough to cope with the current rate of hundreds of thousands of submitted sequences per month.
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli
Authors: Park Joon Young , Lee Sang-Mok , Ebrahim Ali , Scott-Nevros Zoe K , Kim Jaehyung , Yang Laurence , Sastry Anand , Seo Sang Woo , Palsson Bernhard O , Kim Donghyuk 
Published: January 2023

Abstract
The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing experimental conditions, which optimally activate specific TFs. Our model-driven workflow was applied to elucidate transcriptional regulation under nitrogen limitation by Nac and NtrC, in Escherichia coli. We comprehensively predict alternative nitrogen sources, including cytosine and cytidine, which trigger differential activation of Nac using a model-driven workflow. In accordance with the prediction, genome-wide measurements with ChIP-exo and RNA-seq were performed. Integrative data analysis reveals that the Nac and NtrC regulons consist of 97 and 43 genes under alternative nitrogen conditions, respectively. Functional analysis of Nac at the transcriptional level showed that Nac directly down-regulates amino acid biosynthesis and restores expression of tricarboxylic acid (TCA) cycle genes to alleviate nitrogen-limiting stress. We also demonstrate that both TFs coherently modulate α-ketoglutarate accumulation stress due to nitrogen limitation by co-activating amino acid and diamine degradation pathways. A systems-biology approach provided a detailed and quantitative understanding of both TF’s roles and how nitrogen and carbon metabolic networks respond complementarily to nitrogen-limiting stress.
Modeling-Based Response-Guided Hepatitis C Treatment During Pregnancy and Postpartum
Authors: Kushner Tatyana , Nyabanga Custon T , Cotler Scott J , Etzion Ohad , Dahari Harel 
Published: January 2023

Abstract
Treating hepatitis C virus (HCV) in pregnancy would address HCV during prenatal care and potentially reduce the risk of vertical transmission. Response-guided therapy could provide a means to individualize and the reduce duration of HCV treatment during pregnancy. Data from a 27-year-old woman indicated that, pretreatment, HCV was stable and that it dropped in a biphasic manner during sofosbuvir/velpatasvir therapy, reaching target not detected at time of delivery—16 days post–initiation of therapy. Mathematical modeling of measured HCV at days 0, 7, and 14 predicted that cure could have been achieved after 7 weeks of sofosbuvir/velpatasvir, reducing the duration of therapy by 5 weeks.
Predictors of Psychological Distress among Patients with Colorectal Cancer-Related Enterostomy: A Cross-sectional Study
Authors: Li Siqing , Zhong Liping , Zhou Danyan , Zhang Xiumin , Liu Yuxia , Zheng Baojia 
Published: January 2023

ABSTRACT

OBJECTIVE
To identify variables that may predict psychological distress in patients with an enterostomy.

METHODS
Investigators recruited 77 patients with a stoma from a stoma clinic according to the inclusion criteria. Patients’ psychological distress was assessed with the Distress Thermometer (DT) tool, and their personality type was determined by the Eysenck Personality Questionnaire. Researchers also collected demographic and disease-related data. Predictive values were estimated using multiple regression analyses.

RESULTS
The mean DT score of all patients was 5.94 (SD, 1.81), and approximately 85.7% consistently suffered from psychological distress. Being unmarried and having peristomal complications were associated with higher psychological distress, whereas having a monthly income 5,000 ¥ or more was associated with lower levels of distress. Moreover, patients with a melancholic personality type tended to have higher DT scores, which could act as a strong independent predictor for psychological distress.

CONCLUSIONS
The majority of patients with a stoma endured moderate to severe psychological distress during follow-up care. Exploring the related factors that predict the levels of psychological distress could enable clinicians to identify at-risk patients as early as possible and thus provide optimal care for improving patients’ quality of life.