Miracle-dz/UniFAR-FTUs huggingface dataset:
Mistreatment of Vietnamese Elderly by Their Families in the United States

ABSTRACT Generally, research on elder abuse has focused on the elders in mainstream America so that little is known about the nature and scope of elder abuse occurring in the Vietnamese community. This study presents the results of a research project on the relationship of Vietnamese elders residing in Santa Clara County, California and their families. It also explores cultural factors that may be associated with elder mistreatment such as issues of dependency and personal indebtedness. The implications for intervention and prevention are discussed, along with proposed changes in human service programs that could enhance the well-being of Vietnamese elders.
The complete chloroplast genome of brown flatsedge, Cyperus fuscus (Cyperaceae)

Abstract Cyperus fuscus known as brown flatsedge plays an important role in sand fixation and water purification. The first complete chloroplast genome sequences of pioneering plant C. fuscus were reported in this study. The complete chloroplast genome was 167,660 bp in length, containing a large single copy region (LSC) of 79,790 bp and a small single copy region (SSC) of 12,192 bp, which were separated by a pair of 37,839 bp inverted repeat regions (IRs). The chloroplast genome contains 135 genes, including 92 protein-coding genes, eight ribosomal RNA genes, and 35 transfer RNA genes. The overall GC content is 36.3%, while the corresponding values of the LSC, SSC, and IR region are 35.1%, 28.3%, and 38.5%, respectively. Further, the maximum-likelihood phylogenetic analysis showed a strong sister relationship with Cyperus difformis in Cyperaceae. Our findings provide a foundation for further study of chloroplast genome evolution and genetics information in C. fuscus.
DLC1 is a direct target of activated YAP/TAZ that drives collective migration and sprouting angiogenesis

ABSTRACT Endothelial YAP/TAZ (YAP is also known as YAP1, and TAZ as WWTR1) signaling is crucial for sprouting angiogenesis and vascular homeostasis. However, the underlying molecular mechanisms that explain how YAP/TAZ control the vasculature remain unclear. This study reveals that the focal adhesion protein deleted-in-liver-cancer 1 (DLC1) is a direct transcriptional target of the activated YAP/TAZ–TEAD complex. We find that substrate stiffening and VEGF stimuli promote expression of DLC1 in endothelial cells. In turn, DLC1 expression levels are YAP and TAZ dependent, and constitutive activation of YAP is sufficient to drive DLC1 expression. DLC1 is needed to limit F-actin fiber formation, integrin-based focal adhesion lifetime and integrin-mediated traction forces. Depletion of endothelial DLC1 strongly perturbs cell polarization in directed collective migration and inhibits the formation of angiogenic sprouts. Importantly, ectopic expression of DLC1 is sufficient to restore migration and angiogenic sprouting in YAP-depleted cells. Together, these findings point towards a crucial and prominent role for DLC1 in YAP/TAZ-driven endothelial adhesion remodeling and collective migration during angiogenesis. This article has an associated First Person interview with the first author of the paper. Highlighted Article: The focal adhesion protein DLC1 is a direct transcriptional target of YAP/TAZ and TEAD, and is crucial for YAP-driven collective migration and sprouting angiogenesis in endothelial cells.
Roles of Estrogen Signaling in Vertebrate Liver

Estrogen (17b-estradiol; E2) signaling has been implicated in many biological processes, particularly in reproductive biology, organ development and carcinogenesis. E2 plays crucial roles in adult reproductive organ growth and size determination; however, the impact of E2 on non-reproductive organs such as liver is not well understood. In this dissertation work, I have investigated the roles of E2 signaling throughout embryonic liver development and adult liver homeostasis. I demonstrate in Chapter 2 that early activation of E2 signaling during hepatic formation in the zebrafish embryo from 24 hour post fertilization (hpf) progressively decreased liver size, with the most severe impact on hepatic differentiation. These E2 effects are mediated by estrogen receptor 2b (esr2b) as specifically generated esr2b knockout embryos blocked estrogenic effects and had increased liver size. Importantly, while pharmacological blockade of estrogen receptors increased liver size, it negatively impacted cholangiocyte formation, suggesting the potential role of E2 signaling in determining hepatic lineages: promoting biliary tree while suppressing hepatocyte formation. I describe further in Chapter 3 that activation of E2 signaling after hepatic differentiation increased liver size. This increase in liver size induced by E2 exposure was blocked in our generated G protein-coupled estrogen receptor 1 (gper1) knockout embryos, demonstrating that E2 signals via gper1 to drive liver growth. Intriguingly,
Neural signatures of disordered multi-talker speech perception in adults with normal hearing

In social settings, speech waveforms from nearby speakers mix together in our ear canals. The brain unmixes the attended speech stream from the chorus of background speakers using a combination of fast temporal processing and cognitive active listening mechanisms. Multi-talker speech perception is vulnerable to aging or auditory abuse. We found that ∼10% of adult visitors to our clinic have no measurable hearing loss, yet offer a primary complaint of poor hearing. Multi-talker speech intelligibility in these adults was strongly correlated with neural phase locking to frequency modulation (FM) cues, as determined from ear canal EEG recordings. Combining neural temporal fine structure (TFS) processing with pupil-indexed measures of cognitive listening effort could predict most of the individual variance in speech intelligibility thresholds. These findings identify a confluence of disordered bottom-up and top-down processes that predict poor multi-talker speech perception and could be useful in next-generation tests of hidden hearing disorders.
Alibey ve Maden Adaları (Ayvalık-Balıkesir) Çevresi Genç Çökellerinde Gözlenen Bentik Foraminifer Kavkılarındaki Anormal Oluşumlar ve Nedenleri / Abnormal Test Formations Observed in the Benthic Foraminifers from Recent Sediments of Alibey and Maden Islands (Ayvalık-Balıkesir)

Ayvalik kuzeybatisinda bulunan Alibey ve Maden adalari cevresinden alinmis olan 4 kora ait 91 cokel orneginin guncel bentik foraminifer iceriginin belirlenmesi sirasinda kavkilarinda morfolojik bozukluk gosteren cok sayida Peneroplis pertusus, P. planatus, Lobatula lobatula, Ammonia compacta, A. parkinsoniana, Challengerella bradyi, Elphidium complanatum, E. crispum gibi bentik foraminifer bireylerine rastlanilmis tir. Karasal alandaki agir metallerin denizlerdeki biotaya girdisi ve birikmesi , sucul yasam uzerinde cevresel risk olusturur. 20. yuzyil’in ozellikle ikinci yarisinda gerek karasal cevre ve gerekse denize atildigi dusunulen muhtelif atiklar nedeniyle bu alanlarda mangan, kursun ve demir gibi agir metal bakimindan bir kirlenme meydana gelmistir. Keza maden yatagi/yataklarinin calistirilmasi cevredeki foraminifer toplulugunda morfolojik acidan anlamli degisikliklere neden olmustur. Varilan sonuc ise foraminifer kavkilarinda gozlenen ve ekte sunulan anormalliklerin denize ulasan agir metallerin biyolojik etkileri ile gelistigi ve bu durumlarin dogal cevre kirliliginin belirlenmesinde kullanisli bir biogosterici oldugudur. Arastirmanin amaci bolgede sikca rastlanilan bu gibi morfolojik bozukluklarin nedenini aciklamak ve benzer olusumlara sebep olan diger etkenler ile karsilastirmaktir.
Analysis of hindgut bacterial phyla frequency and diversity in subterranean termites exposed to chitosan-treated wood

The termite hindgut contains a microbial community that symbiotically aids in digestion of lignocellulosic materials. For better understanding of the dynamics of the bacteria-termite relationship, a species survey of bacterial hindgut microbes in subterranean termites ( Reticulitermes flavipes : Kollar) collected from Louisville, Mississippi was performed after exposure to chitosan-treated and control (water-treated) wood samples. Total genomic DNA was isolated from termite hindguts, amplified and 16S ribosomal RNA (rRNA) gene fragments were analyzed using next-generation sequencing techniques. Twenty-six bacteria phyla were identified in both treatment groups, with five bacteria phyla showing significantly differences in abundance between the chitosan-treated and control groups. These results suggest that there was a treatment driven effect on the hindgut bacteria diversity.
Coral-bacteria associations-determining the role of Chemotaxis

Bacteria play a fundamental role in determining the health and ecology of corals. The important functions of the bacterial consortia inhabiting the coral holobiont include chemical cycling, provision of a food resource for the host, as well as a potential role in coral disease. Indeed, pathogenic bacteria have been implicated as an important cause of the world-wide decline in coral health. Currently, however, little is known about the mechanisms involved in establishing an association between corals and bacteria. The relative abundance of bacterial communities associated with the branching coral Pocillopora damicornis was examined under laboratory conditions in aquaria and on Heron Island, where an additional species Montipora digitata was also monitored. Bacterial concentrations associated with the surface of corals were compared to the surrounding water using flow cytometry. On Heron Island, there was no significant difference observed in bacterial abundances between the healthy Coral Surface Microlayer (CSM) and those of the surrounding seawater for both P. damicornis and M. digitata. However, there were significantly more bacteria associated with the CSM of diseased specimens of both P. damicornis and M. Digitata. To examine the potential mechanism behind this coral-bacteria association, we performed chemotaxis experiments where the extent of bacterial chemotaxis towards chemicals expected to be associated with the coral holobiont were tested using a modified capillary assay. Chemoattractants tested included zooxanthellae extracellular excretions, as well as organic compounds including a variety of amino acids and sugars, dimethyl sulphide (DMS) and dimethylsulfonopropionate (DMSP). In all cases, coral associated bacteria from Heron Island exhibited significantly higher levels of chemotaxis than non-coral associated bacteria, from both the laboratory and the field. Bacterial attraction towards the sugars and amino acids tested led to bacterial concentrations that reached 176 and 186 times higher within chemoattractant chambers respectively, in comparison to background
Multi-Trait and Trait-Assisted Genomic Prediction of Winter Wheat Quality Traits Using Advanced Lines from Four Breeding Cycles

Genetically correlated traits can be used for improving predictive abilities of genomic predictions including several traits in multi-trait models. Here, the wheat quality traits thousand-kernel weight, grain protein content, Zeleny sedimentation, and falling number were phenotyped in 1152 advanced winter wheat lines from four cycles of a commercial breeding program. Multi-trait and trait-assisted genomic prediction models including two or four traits were studied and compared with single-trait models. In the trait-assisted genomic predictions, breeding values of the trait of interest were predicted for lines that had been phenotyped for additional traits. Predictive abilities of single-trait models ranged from 0.5 for thousand-kernel weight to 0.65 for falling number based on 10-fold cross-validations. Predictive abilities were in most cases not significantly different between single- and multi-trait models, when no phenotypic data was included for lines in the validation set. However, predictive abilities for grain protein content increased when using trait-assisted models, where the phenotypic data for Zeleny sedimentation or falling number were available for the lines in the validation set. The trait-assisted models also resulted in increased predictive abilities for Zeleny sedimentation, when phenotypic data for grain protein content was included. The latter situation could be relevant for breeding programs for improving wheat quality.
Notch signaling regulates Akap12 expression and primary cilia length during renal tubule morphogenesis

Alagille syndrome patients present with loss of function mutations in either JAG1 or NOTCH2. About 40-50% of patients have kidney abnormalities, with multi-cystic, dysplastic kidneys being one of the more frequent kidney defects. Additionally, gain-of-function mutations in NOTCH2 are associated with cystic kidneys in Hajdu-Cheney syndrome patients. Conditional inactivation of Notch1, Notch2, or RBPJ within the nephrogenic lineage impairs nephrogenesis and produces proximal tubule cysts in mice. How perturbations in Notch signaling cause renal tubular cysts remains unclear. Here we have determined that inhibition of Notch signaling in the kidney increases Akap12 expression. Ectopic expression of Akap12 in renal epithelia results in abnormally long primary cilia similar to those observed in Notch-signal-deficiency. Both loss of Notch signaling and elevated Akap12 expression disrupt the ability of renal epithelial cells to form spherical structures with a single lumen when grown embedded in matrix. We conclude that Notch signaling regulates Akap12 expression to ensure normal primary cilia length and renal epithelial morphogenesis, and suggest that diseases associated with defective Notch signaling, such as Alagille syndrome, maybe mechanistically related to ciliopathies. Translational Statement The current study examines how a reduction in Notch signaling results in abnormal renal tubule formation, as occurs in Alagille Syndrome patients with mutations in JAG1 or NOTCH2. The finding that reduced Notch signaling results in abnormally long cilia is suggestive that some of the clinical manifestations in Alagille Syndrome, such as small cystic kidneys, may originate due to defective cilia function. Linking Notch to primary cilia also opens up the possibility that coinheritance of mutations in ciliopathy genes along with a mutation in JAG1 or NOTCH2 may enhance the severity of the clinical phenotypes such as cystic kidney disease and may explain the variable occurrence and onset of kidney disease among Alagille Syndrome patients.
Face Selective Neural Activity: comparison between fixed and free viewing

Event Related paradigms (ERPs) are widely used to study category-selective EEG responses to visual stimuli, such as the face-selective N170 component. While allowing for good experimental control these paradigms ignore the dynamic role of eye-movements in natural vision. Fixation-related potentials (FRPs) obtained using simultaneous EEG and eye-tracking overcome this limitation. While various studies have used FRPs to study processes such as lexical processing, target detection and attention allocation, no study has directly examined categorical visual recognition in free-viewing conditions. The goal of this study was to compare the well-known face-sensitive activity evoked by stimulus abrupt appearance (N170 component) with that evoked by self-controlled fixations on a stimulus. Twelve subjects were studied in three experimental conditions: Free-viewing (FRPs), Cued-viewing(FRPs) and Control (ERPs). We used a multiple regression GLM approach to disentangle overlapping components. Our results show that the N170 face differential effect (face vs. non-face) is evident for the first fixation on a stimulus, whether it follows a self-generated saccade or stimulus appearance at fixation point. Whereas the N170 differential effect has similar topography across viewing conditions, there are major differences between ERP and FRP activity within each stimulus category. We hypothesized that the fixation-related Lambda complex may overlap the N170 in FRPs, and establish the plausibility of this account using hypothesis-driven dipole simulations. This study establishes the use of the N170 effect as a signature of face detection in free viewing experiments while highlighting the importance of accounting for fixation-specific effects.
Climate change and aquaculture: considering adaptation potential

Increases in global population and seafood demand are occurring simultaneously with fisheries decline in an era of rapid climate change. Aquaculture is well positioned to help meet the world’s future seafood needs, but heavy reliance of most global aquaculture on the ambient environment and ecosystem services suggests inherent vulnerability to climate change effects. There are, however, opportunities for adaptation. Engineering and management solutions can reduce exposure to stressors or mitigate stressors through environmental control. Epigenetic adaptation may have the potential to improve stressor tolerance through parental or early life stage exposure. Stressor-resistant traits can be genetically selected for, and maintaining adequate population variability can improve resilience and overall fitness. Information at appropriate time scales is crucial for adaptive response, such as real-time data on stressor levels and/or species’ responses, early warning of deleterious events, or prediction of longer-term change. Diet quality and quantity have the potential to meet increasing energetic and nutritional demands associated with mitigating the effects of abiotic and biotic climate change stressors. Research advancements in understanding how climate change affects aquaculture will benefit most from a combination of empirical studies, modelling approaches, and observations at the farm level. Research to support aquaculture adaptation requires an increasing amount of environmental data to guide biological response studies for regional applications. Increased experimental complexity, resources, and duration will be necessary to better understand the effects of multiple stressors. Ultimately, in order for aquaculture sectors to move beyond short-term coping responses, governance initiatives incorporating the changing needs of stakeholders, users, and culture ecosystems as a whole are required to facilitate planned climate change adaptation and mitigation.
Multiple separate cases of pseudogenized meiosis genes Msh4 and Msh5 in Eurotiomycete fungi: associations with Zip3 sequence evolution and homothallism, but not Pch2 losses

The overall process of meiosis is conserved in many species, including some lineages that have lost various ancestrally present meiosis genes. The extent to which individual meiosis gene losses are independent from or dependent on one another is largely unknown. Various Eurotiomycete fungi were investigated as a case system of recent meiosis gene losses after BLAST and synteny comparisons found Msh4, Msh5, Pch2, and Zip3 to be either pseudogenized or undetected in Aspergillus nidulans yet intact in congeners such as A. fumigatus. Flanking gene-targeted degenerate PCR primers applied to 9 additional Aspergillus species found (i) Msh4, Msh5, and Zip3 pseudogenized in A. rugulosus (sister taxon to A. nidulans) but intact in all other amplified sequences; and (ii) Pch2 not present at the syntenic locus in most of the 9 species. Topology tests suggested two independent Pch2 losses in genus Aspergillus, neither directly coinciding with pseudogenization of the other three genes. The A. nidulans-A. conjunctus clade Pch2 loss was not associated with significant Ka/Ks changes for Msh4, Msh5, or Zip3; this suggests against prior Pch2 loss directly altering sequence evolution constraints on these three genes. By contrast, Zip3 Ka/Ks tended to be elevated in several other Eurotiomycete fungi with independently pseudogenized Msh4 and Msh5 (Talaromyces stipitatus, Eurotium herbariorum). The coinciding Ka/Ks elevation and/or clear pseudogenization of Zip3 in taxa with pseudogenized Msh4 and Msh5 is consistent with some degree of molecular coevolution. Possible molecular, environmental, and life history variables (e.g., homothallism) that may be associated with these numerous independent meiosis gene losses (Msh4: 3, Msh5: 3, Zip3: ≥ 1, Pch2: 4) are discussed.
Systematic identification of engineered methionines and oxaziridines for efficient, stable, and site-specific antibody bioconjugation

Significance Site-specific chemical modification of proteins remains a critical need for bioconjugation. Here we explore the key parameters needed for efficient, selective, and stable modification of methionine using recently developed oxaziridine reagents, called ReACT. We systematically tested various oxaziridine compounds, and scanned accessible and buried sites in a therapeutic antibody for breast cancer to determine the chemical and structural parameters for most stable and efficient modification. We show these adducts are highly stable over days and can support the delivery of toxic payloads to regress tumors in animals. These studies on this important chemical modification expand our capability to site-specifically modify proteins and antibodies for many applications. The field of chemical modification of proteins has been dominated by random modification of lysines or more site-specific labeling of cysteines, each with attendant challenges. Recently, we have developed oxaziridine chemistry for highly selective modification of methionine called redox-activated chemical tagging (ReACT) but have not broadly tested the molecular parameters for efficient and stable protein modification. Here we systematically scanned methionines throughout one of the most popular antibody scaffolds, trastuzumab, used for antibody engineering and drug conjugation. We tested the expression, reactivities, and stabilities of 123 single engineered methionines distributed over the surface of the antibody when reacted with oxaziridine. We found uniformly high expression for these mutants and excellent reaction efficiencies with a panel of oxaziridines. Remarkably, the stability to hydrolysis of the sulfimide varied more than 10-fold depending on temperature and the site of the engineered methionine. Interestingly, the most stable and reactive sites were those that were partially buried, presumably because of their reduced access to water. There was also a 10-fold variation in stability depending on the nature of the oxaziridine, which was determined to be inversely correlated with the electrophilic nature of the sulfimide. Importantly, the stabilities of the best analogs were sufficient to support their use as antibody drug conjugates and potent in a breast cancer mouse xenograft model over a month. These studies provide key parameters for broad application of ReACT for efficient, stable, and site-specific antibody and protein bioconjugation to native or engineered methionines.