Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Two Nonrearranging IgSF Genes in Chicken Reveals a Novel Family of Putative Remnants of an Antigen Receptor Precursor

In this study, we identified a pair of nonrearranging VJ-joined Ig superfamily genes, termed putative remnants of an Ag receptor precursor (PRARP) genes, in chicken. Both genes encode a single V-set Ig domain consisting of a canonical J-like segment and a potential immunoreceptor tyrosine-based inhibitory or switch motif in the cytoplasmic region. In vitro experiments showed that both genes were expressed at the cell surface as membrane proteins, and their recombinant products formed a monomer and a disulfide-linked homodimer or a heterodimer. These two genes were mainly expressed in B and T cells and were upregulated in response to stimulation with poly(I:C) in vitro and vaccination in vivo. Orthologs of PRARP have been identified in bony fish, amphibians, reptiles, and other birds, and a V-C1 structure similar to that of Ig or TCR chains was found in all these genes, with the exception of those in avian species, which appear to contain degenerated C1 domains or divergent Ig domains. Phylogenetic analyses suggested that the newly discovered genes do not belong to any known immune receptor family and appear to be a novel gene family. Further elucidation of the functions of PRARP and their origin might provide significant insights into the evolution of the immune system of jawed vertebrates.
A spatiotemporally regulated transcriptional complex underlies heteroblastic development of leaf hairs in Arabidopsis thaliana

Heteroblasty refers to a phenomenon that a plant produces morphologically or functionally different lateral organs in an age‐dependent manner. In the model plant Arabidopsis thaliana, the production of trichomes (epidermal leaf hairs) on the abaxial (lower) side of leaves is a heteroblastic mark for the juvenile‐to‐adult transition. Here, we show that the heteroblastic development of abaxial trichomes is regulated by a spatiotemporally regulated complex comprising the leaf abaxial fate determinant (KAN1) and the developmental timer (miR172‐targeted AP2‐like proteins). We provide evidence that a short‐distance chromatin loop brings the downstream enhancer element into close association with the promoter elements of GL1, which encodes a MYB transcription factor essential for trichome initiation. During juvenile phase, the KAN1‐AP2 repressive complex binds to the downstream sequence of GL1 and represses its expression through chromatin looping. As plants age, the gradual reduction in AP2‐like protein levels leads to decreased amount of the KAN1‐AP2 complex, thereby licensing GL1 expression and the abaxial trichome initiation. Our results thus reveal a novel molecular mechanism by which a heteroblastic trait is governed by integrating age and leaf polarity cue in plants.
Clarification of generic and species boundaries for Metarhizium and related fungi through multigene phylogenetics

The genus Metarhizium historically refers to green-spored asexual insect pathogenic fungi. Through culturing and molecular methods, Metarhizium has been linked to Metacordyceps sexual states. Historically fungal nomenclature has allowed separate names for the different life stages of pleomorphic fungi. However, with the move to one name for one fungus regardless of life stage, there is a need to determine which name is correct. For Metarhizium the situation is complicated by the fact that Metacordyceps sexual states are interspersed among additional asexual genera, including Pochonia, Nomuraea and Paecilomyces. Metarhizium has priority as the earliest available name, but delimiting the boundaries of this genus remains problematic. To clarify relationships among these taxa we have obtained representative material for each genus and established a molecular dataset of the protein-coding genes BTUB, RPB1, RPB2 and TEF. The resulting phylogeny supports Metarhizium combining the majority of species recognized in Metacordyceps as well as the green-spored Nomuraea species and those in the more recently described genus Chamaeleomyces. Pochonia is polyphyletic, and we restrict the definition of this genus to those species forming a monophyletic clade with P. chlamydosporia, and the excluded species are transferred to Metapochonia gen. nov. It is our hope that this unified concept of sexual and asexual states in Metarhizium will foster advances in communication and understanding the unique ecologies of the associated species.
Transient heat transfer in dental implants for thermal necrosis-aided implant removal: A 3D finite element analysis.

Removal of osseointegrated but otherwise failed (mechanical failure, mispositioning, aesthetics, etc.) dental implants is a traumatic process resulting in loss of healthy bone and complicating the treatment process. The traumatic effects of implant removal can be reduced by weakening the implant-bone attachment. Thermal necrosis-aided implant removal has been proposed as a minimally invasive method towards this end. In this method; an electrocautery tip is contacted to the implant to increase the temperature to 47oC and generate a limited and controlled thermal necrosis at the bone-implant interface. So far, no controlled studies have been performed to investigate the optimal clinical parameters for this method. In this study, we aimed to investigate, using Finite Element Analysis method, the optimal settings to achieve intentional thermal necrosis on three implant systems, at 5W and 40W device power and with different size tips. The temperature increase of the implants at 40W power was very sudden (<0.5 seconds) and as the bone reached 47oC, the implants were at unacceptable temperatures. At 5W power, temperature increase of the implants happened at manageable durations (< 1 second). Moreover, the temperature increase was even slower with larger implants and larger tips sizes. Therefore, low power settings must be used for thermal necrosis-aided implant removal. Also, the size of the implant and the tip must be taken into consideration in deciding the duration of contact with the electrocautery tip and the implant.
Using Microsaccades to Estimate Task Difficulty During Visual Search of Layered Surfaces

We develop an approach to using microsaccade dynamics for the measurement of task difficulty/cognitive load imposed by a visual search task of a layered surface. Previous studies provide converging evidence that task difficulty/cognitive load can influence microsaccade activity. We corroborate this notion. Specifically, we explore this relationship during visual search for features embedded in a terrain-like surface, with the eyes allowed to move freely during the task. We make two relevant contributions. First, we validate an approach to distinguishing between the <italic>ambient</italic> and <italic>focal</italic> phases of visual search. We show that this spectrum of visual behavior can be quantified by a single previously reported estimator, known as Krejtz's <inline-formula><tex-math notation="LaTeX">$\mathcal {K}$</tex-math><alternatives><mml:math><mml:mi mathvariant="script">K</mml:mi></mml:math><inline-graphic xlink:href="duchowski-ieq1-2901881.gif"/></alternatives></inline-formula> coefficient. Second, we use ambient/focal segments based on <inline-formula><tex-math notation="LaTeX">$\mathcal {K}$</tex-math><alternatives><mml:math><mml:mi mathvariant="script">K</mml:mi></mml:math><inline-graphic xlink:href="duchowski-ieq2-2901881.gif"/></alternatives></inline-formula> as a moderating factor for microsaccade analysis in response to task difficulty. We find that during the focal phase of visual search (a) microsaccade magnitude increases significantly, and (b) microsaccade rate decreases significantly, with increased task difficulty. We conclude that the combined use of <inline-formula><tex-math notation="LaTeX">$\mathcal {K}$</tex-math><alternatives><mml:math><mml:mi mathvariant="script">K</mml:mi></mml:math><inline-graphic xlink:href="duchowski-ieq3-2901881.gif"/></alternatives></inline-formula> and microsaccade analysis may be helpful in building effective tools that provide an indication of the level of cognitive activity within a task while the task is being performed.
ESA1 Is Involved in Embryo Sac Abortion in Interspecific Hybrid Progeny of Rice1

ESA1 is involved in embryo sac abortion in hybrid backcross progeny derived from common wild rice and cultivated rice. The emergence of sterile individuals in the hybrid backcross progeny of wild and cultivated rice limits the use of wild rice alleles for improving cultivated rice, but the molecular mechanisms underlying this sterility remain unclear. Here, we identified the semisterile introgression line YIL42, derived from a cross between the indica rice variety Teqing (Oryza sativa) and Oryza rufipogon accession YJCWR (Yuanjiang common wild rice), which exhibits semisterility. Using positional cloning, we isolated EMBRYO SAC ABORTION 1 (ESA1), which encodes a nuclear-membrane localized protein containing an armadillo repeat domain. A mutation in ESA1 at position 1819 (T1819C) converts a stop codon into an Arg (R) codon, causing delayed termination of protein translation. Analysis of transgenic lines indicated that the difference in ESA1 protein structure between O. rufipogon–derived ESA1 and Teqing-derived esa1 affects female gamete abortion during early mitosis. Fertility investigation and expression analysis indicated that the interaction between ESA1T1819 and unknown gene(s) of Teqing affects spikelet fertility of the hybrid backcross progeny. The ESA1T1819 allele is present in O. rufipogon but absent in O. sativa, suggesting that variation in ESA1 may be associated with interspecific hybrid incompatibility between wild and cultivated rice. Our findings provide insight into the molecular mechanism underlying female sterility, which is useful for improving the panicle seed setting rate of rice and for developing a strategy to overcome interspecific hybrid sterility between cultivated rice and wild rice.
PDMS Microlenses for Focusing Light in Narrow Band Imaging Diagnostics

Minimally invasive medical devices can greatly benefit from Narrow Band Imaging (NBI) diagnostic capabilities, as different wavelengths allow penetration of distinct layers of the gastrointestinal tract mucosa, improving diagnostic accuracy and targeting different pathologies. An important performance parameter is the light intensity at a given power consumption of the medical device. A method to increase the illumination intensity in the NBI diagnostic technique was developed and applied to minimally invasive medical devices (e.g., endoscopic capsules), without increasing the size and power consumption of such instruments. Endoscopic capsules are generally equipped with light-emitting diodes (LEDs) operating in the RGB (red, green, and blue) visible light spectrum. A polydimethylsiloxane (PDMS) µ-lens was designed for a maximum light intensity at the target area of interest when placed on top of the LEDs. The PDMS µ-lens was fabricated using a low-cost hanging droplet method. Experiments reveal an increased illumination intensity by a factor of 1.21 for both the blue and green LEDs and 1.18 for the red LED. These promising results can increase the resolution of NBI in endoscopic capsules, which can contribute to early gastric lesions diagnosis.
Yogurt: Technology and Biochemistry 1.

This review considers the physical and chemical changes which occur during yogurt manufacture as a result of processing and microbial fermentation. Changes produced during processes, such as heat treatment and physical manipulations, are reviewed. Microbial fermentation is discussed in terms of the characteristics of the yogurt organisms, Lactobacillus bulgaricus and Streptococcus thermophilus , and the biochemical reactions involved in carbohydrate metabolism, flavor production, proteolysis and lipolysis.
Biogeography of the endosymbiotic dinoflagellates (Symbiodiniaceae) community associated with the brooding coral Favia gravida in the Atlantic Ocean

Zooxanthellate corals live in symbiosis with phototrophic dinoflagellates of the family Symbiodiniaceae, enabling the host coral to dwell in shallow, nutrient-poor marine waters. The South Atlantic Ocean is characterized by low coral diversity with high levels of endemism. However, little is known about coral–dinoflagellate associations in the region. This study examined the diversity of Symbiodiniaceae associated with the scleractinian coral Favia gravida across its distributional range using the ITS-2 marker. This brooding coral endemic to the South Atlantic can be found across a wide range of latitudes and longitudes, including the Mid-Atlantic islands. Even though it occurs primarily in shallower environments, F. gravida is among the few coral species that live in habitats with extreme environmental conditions (high irradiance, temperature, and turbidity) such as very shallow tide pools. In the present study, we show that F. gravida exhibits some degree of flexibility in its symbiotic association with zooxanthellae across its range. F. gravida associates predominantly with Cladocopium C3 (ITS2 type Symbiodinium C3) but also with Symbiodinium A3, Symbiodinium linucheae (ITS2 type A4), Cladocopium C1, Cladocopium C130, and Fugacium F3. Symbiont diversity varied across biogeographic regions (Symbiodinium A3 and S. linucheae were found in the Tropical Eastern Atlantic, Cladocopium C1 in the Mid-Atlantic, and other subtypes in the Southwestern Atlantic) and was affected by local environmental conditions. In addition, Symbiodiniaceae diversity was highest in a southwestern Atlantic oceanic island (Rocas Atoll). Understanding the relationship between corals and their algal symbionts is critical in determining the factors that control the ecological niches of zooxanthellate corals and their symbionts, and identifying host-symbiont pairs that may be more resistant to environmental changes.
Long-Term Oncological Outcomes in Laparoscopic Versus Open Pancreaticoduodenectomy for Pancreatic Cancer: A Systematic Review and Meta-Analysis.

Background: Short-term outcomes after laparoscopic pancreaticoduodenectomy (LPD) seem promising, but long-term outcomes of LPD for pancreatic cancer (PC) warrant further investigation. Methods: A systematic research of various databases was performed to identify studies analyzing long-term outcomes in LPD versus open pancreaticoduodenectomy (OPD) for PC. Survival parameters of overall survival (OS) and disease-free survival (DFS) were extracted. The search was last conducted before May 23, 2018. Results: A total of 10 studies involving 11,180 patients (1437 in LPD and 9743 in OPD) met the final inclusion criteria. Pooled analyses showed that LPD was associated with longer DFS compared with OPD (hazard ratio [HR]: 0.77, 95% confidence interval [CI]: 0.61 to 0.98, P = .033). No significant difference in OS was found between LPD and OPD (HR: 0.98, 95% CI: 0.90 to 1.07, P = .672). In addition, patients of LPD had much shorter time to receive postoperative adjuvant chemotherapy compared with OPD (weighted mean difference: -10.17, 95% CI: -17.90 to -2.45, P = .010). Discussion: With regard to long-term survival, LPD is comparable with OPD for PC. Furthermore, LPD is associated with longer DFS compared with OPD. Future well-designed, randomized controlled trials with longer follow-up are still essential to further demonstrate the advantages of LPD for PC.
Inhibition of the PERK-Dependent Unfolded Protein Response Signaling Pathway Involved in the Pathogenesis of Alzheimer's Disease.

OBJECTIVES There is a body of evidence that neurodegenerative disease entities are directly correlated with the perturbations on the molecular level. Hence, the ER stress-mediated Unfolded Protein Response (UPR) is activated resulting in PERK-dependent phosphorylation of the Eukaryotic initiation factor 2 (eIF2α). Thus, the levels of ATF4 and CHOP proteins are significantly increased, which subsequently switches the pro-adaptive branch of the UPR into the pro-apoptotic directly leading to neuronal loss and initiation of the neurodegenerative process. The aim of the presented study was the evaluation of the biological activity of highly specific, small-molecule inhibitors of the PERKdependent UPR signaling pathway. METHODS The study was conducted on rat astrocytic DI TNC1 cell line. The level of p-eIF2α was measured by Western blot technique, the cytotoxicity of the investigated compound was assessed by the MTT assay and using the FITC-conjugated Annexin V (Annexin V-FITC) to indicate apoptosis and propidium iodide (PI) to indicate necrosis. The effect of tested compound on cell cycle progression was measured by flow cytometry, where the PI-labelled nuclei were analysed for DNA content. RESULTS As a result one of the investigated compound LDN-0060609 triggers a significant inhibition of the eIF2α phosphorylation in DI TNC1 cell line. Moreover, we showed that compound LDN-0060609 is non-cytotoxic and has no effect on cell cycle progression. CONCLUSION In conclusion, LDN-0060609 may constitute a novel, targeted treatment approach against neurodegenerative diseases, including Alzheimer's disease (AD), where pathogenesis and progression are closely associated with the overactivation of the PERK-dependent UPR signaling pathway.
Identification of barriers, facilitators and system-based implementation strategies to increase teleophthalmology use for diabetic eye screening in a rural US primary care clinic: a qualitative study

Objective Teleophthalmology for diabetic eye screening is an evidence-based intervention substantially underused in US multipayer primary care clinics, even when equipment and trained personnel are readily available. We sought to identify patient and primary care provider (PCP) barriers, facilitators, as well as strategies to increase teleophthalmology use. Design We conducted standardised open-ended, individual interviews and analysed the transcripts using both inductive and directed content analysis to identify barriers and facilitators to teleophthalmology use. The Chronic Care Model was used as a framework for the development of the interview guide and for categorising implementation strategies to increase teleophthalmology use. Setting A rural, US multipayer primary care clinic with an established teleophthalmology programme for diabetic eye screening. Participants We conducted interviews with 29 participants (20 patients with diabetes and 9 PCPs). Results Major patient barriers to teleophthalmology use included being unfamiliar with teleophthalmology, misconceptions about diabetic eye screening and logistical challenges. Major patient facilitators included a recommendation from the patient’s PCP and factors related to convenience. Major PCP barriers to referring patients for teleophthalmology included difficulty identifying when patients are due for diabetic eye screening and being unfamiliar with teleophthalmology. Major PCP facilitators included the ease of the referral process and the communication of screening results. Based on our results, we developed a model that maps where these key patient and PCP barriers occur in the teleophthalmology referral process. Patients and PCPs also identified implementation strategies to directly address barriers and facilitators to teleophthalmology use. Conclusions Patients and PCPs have limited familiarity with teleophthalmology for diabetic eye screening. PCPs were expected to initiate teleophthalmology referrals, but reported significant difficulty identifying when patients are due for diabetic eye screening. System-based implementation strategies primarily targeting PCP barriers in conjunction with improved patient and provider education may increase teleophthalmology use in rural, US multipayer primary care clinics.
Effect of Irrigation and Soil Water Stress on Densities of Macrophomina phaseolina in Soil and Roots of Two Soybean Cultivars.

The effects of irrigation and soil water stress on Macrophomina phaseolina microsclerotial (MS) densities in the soil and roots of soybean were studied in 1988, 1989, and 1990. Soybean cvs. Davis and Lloyd received irrigation until flowering (TAR2), after flowering (IAR2), full season (FSI), or not at all (NI). Soil water matric potentials at 15- and 30-cm depths were recorded throughout the growing season and used to schedule irrigation. Soil MS densities were determined at the beginning of each season. Root MS densities were determined periodically throughout the growing season. Microsclerotia were present in the roots of irrigated as well as nonirrigated soybean within 6 weeks after planting. By vegetative growth stage V13, these densities reached relatively stable levels in the NI and FSI treatments (2.23 to 2.35 and 1.35 to 1.63 log [microsclerotia per gram of dry root], respectively) through reproductive growth stage R6. After R6, irrigation was discontinued and root densities of microsclerotia increased in all treatments. Initiation (IAR2) or termination (TAR2) of irrigation at R2 resulted in significant changes in root MS densities, with densities reaching levels intermediate between those of FSI and NI treatments. Year to year differences in root colonization reflected differences in soil moisture due to rainfall. The rate of root colonization in response to soil moisture stress decreased with plant age. Root colonization was significantly greater in Davis than Lloyd at R5 and R8. This was reflected in a trend toward higher soil densities of M. phaseolina at planting in plots planted with Davis than in plots planted with Lloyd. Although no charcoal rot symptoms in the plant were observed in this study, these results indicated that water management can limit, but not prevent, colonization of soybean by M. phaseolina, that cultivars differ in colonization, and that these differences may affect soil densities of the fungus.
A branching gene regulatory network dictating different aspects of a neuronal cell identity

ABSTRACT The nervous system displays a daunting cellular diversity. Neuronal subtypes differ from each other in several aspects, including their neurotransmitter expression and axon projection. These aspects can converge, but can also diverge, such that neurons expressing the same neurotransmitter may project axons to different targets. It is not well understood how regulatory programs converge/diverge to associate/dissociate different cell fate features. Studies of the Drosophila Tv1 neurons have identified a regulatory cascade, ladybird early→collier→apterous/eyes absent→dimmed, that specifies Tv1 neurotransmitter expression. Here, we conduct genetic and transcriptome analysis to address how other aspects of Tv1 cell fate are governed. We find that an initiator terminal selector gene triggers a feedforward loop that branches into different subroutines, each of which establishes different features of this one unique neuronal cell fate. Summary: The Drosophila Tv1 neuropeptide neuron is specified, not by one single regulatory gene, but by several regulators acting in different combinations to govern different aspects of this cell fate.