Miracle-dz/UniFAR-FTUs huggingface dataset:
The zinc cluster transcription factor Czf1 regulates cell wall architecture and integrity in Candida albicans

The fungal cell wall is essential for the maintenance of cellular integrity and mediates interactions of the cells with the environment. It is a highly flexible organelle whose composition and organization is modulated in response to changing growth conditions. In the pathogenic yeast Candida albicans, a network of signaling pathways regulates the structure of the cell wall, and mutants with defects in these pathways are hypersensitive to cell wall stress. By harnessing a library of genetically activated forms of all C. albicans zinc cluster transcription factors, we found that a hyperactive Czf1 rescued the hypersensitivity to cell wall stress of different protein kinase deletion mutants. The hyperactive Czf1 induced the expression of many genes with cell wall‐related functions and caused visible changes in the cell wall structure. C. albicans czf1Δ mutants were hypersensitive to the antifungal drug caspofungin, which inhibits cell wall biosynthesis. The changes in cell wall architecture caused by hyperactivity or absence of Czf1 resulted in an increased recognition of C. albicans by human neutrophils. Our results show that Czf1, which is known as a regulator of filamentous growth and white‐opaque switching, controls the expression of cell wall genes and modulates the architecture of the cell wall.
Homeodomain proteins POU‐M2, antennapedia and abdominal‐B are involved in regulation of the segment‐specific expression of the clip‐domain serine protease gene CLIP13 in the silkworm, Bombyx mori

Clip‐domain serine proteases (CLIPs) play important roles in insect innate immunity and development. Our previous studies indicated that CLIP13, an epidermis‐specific gene, was involved in cuticle remodeling during molting and metamorphosis in the silkworm, Bombyx mori. However, the transcriptional regulatory mechanism and regulatory pathways of CLIP13 remained unclear. In the present study, we investigated CLIP13 expression and the regulation pathway controlled by 20‐hydroxyecdysone (20E) in the silkworm. At the transcriptional level, expression of CLIP13 exhibited pronounced spatial and temporal specificity in different regions of the epidermis; homeodomain transcription factors POU‐M2, antennapedia (Antp), and abdominal‐B (Abd‐B) showed similar expression change trends as CLIP13 in the head capsule, thorax, and abdomen, respectively. Furthermore, results of cell transfection assays, electrophoretic mobility shift assays, and chromatin immunoprecipitation demonstrated that POU‐M2, Antp, and Abd‐B were involved in the transcriptional regulation of CLIP13 by directly binding to their cis‐response elements in CLIP13 promoter. RNA interference‐mediated silencing of POU‐M2, Antp, and Abd‐B led to a decrease of CLIP13 expression in the head capsule, the epidermis of the 1st to 3rd thoracic segments and the 7th to 10th abdominal segments, respectively. Consistent with CLIP13, 20E treatment significantly upregulated expression of POU‐M2, Antp, and Abd‐B in the silkworm epidermis. Taken together, these data suggest that 20E positively regulates transcription of CLIP13 via homeodomain proteins POU‐M2, Antp, and Abd‐B in different regions of the silkworm epidermis during metamorphosis, thus affecting the molting process. Our findings provide new insight into the functions of homeodomain transcription factors in insect molting.
Effects of an Interprofessional Communication Approach on Support Needs, Quality of Life, and Mood of Patients with Advanced Lung Cancer: A Randomized Trial

Abstract Background To address the support needs of newly diagnosed patients with lung cancer with limited prognosis, the Milestone Communication Approach (MCA) was developed and implemented. The main elements of the MCA are situation‐specific conversations along the disease trajectory conducted by an interprofessional tandem of physician and nurse. The aim of the study was to evaluate the effects of MCA on addressing support needs, quality of life, and mood as compared with standard oncological care. Patients and Methods A randomized trial was conducted with baseline assessment and follow‐up assessments at 3, 6, and 9 months in outpatients with newly diagnosed lung cancer stage IV at a German thoracic oncology hospital. The primary outcome was the Health System and Information Needs subscale of the Short Form Supportive Care Needs Survey (SCNS‐SF34‐G) at 3‐month follow‐up. Secondary outcomes included the other subscales of the SCNS‐SF34‐G, the Schedule for the Evaluation of Individual Quality of Life, the Functional Assessment of Cancer Therapy lung module, the Patient Health Questionnaire for Depression and Anxiety, and the Distress Thermometer. Results At baseline, 174 patients were randomized, of whom 102 patients (MCA: n = 52; standard care: n = 50) provided data at 3‐month follow‐up. Patients of the MCA group reported lower information needs at 3‐month follow‐up (mean ± SD, 33.4 ± 27.5; standard care, 43.1 ± 29.9; p = .033). No effects were found for secondary outcomes. Conclusion MCA lowered patient‐reported information needs but did not have other effects. MCA contributed to tailored communication because an adequate level of information and orientation set the basis for patient‐centered care. Implications for Practice By addressing relevant issues at predefined times, the Milestone Communication Approach provides individual patient‐centered care facilitating the timely integration of palliative care for patients with a limited prognosis. The needs of patients with lung cancer must be assessed and addressed throughout the disease trajectory. Although specific topics may be relevant for all patients, such as information about the disease and associated health care, situations of individual patients and their families must be considered. Additionally, using the short form of the Supportive Care Needs Survey in clinical practice to identify patients’ problems might support individually targeted communication and preference‐sensitive care.
Multi-task Learning-based All-in-one Collaboration Framework for Degraded Image Super-resolution

In this article, we address the degraded image super-resolution problem in a multi-task learning (MTL) manner. To better share representations between multiple tasks, we propose an all-in-one collaboration framework (ACF) with a learnable “junction” unit to handle two major problems that exist in MTL—“How to share” and “How much to share. ” Specifically, ACF consists of a sharing phase and a reconstruction phase. Considering the intrinsic characteristic of multiple image degradations, we propose to first deal with the compression artifact, motion blur, and spatial structure information of the input image in parallel under a three-branch architecture in the sharing phase. Subsequently, in the reconstruction phase, we up-sample the previous features for high-resolution image reconstruction with a channel-wise and spatial attention mechanism. To coordinate two phases, we introduce a learnable “junction” unit with a dual-voting mechanism to selectively filter or preserve shared feature representations that come from sharing phase, learning an optimal combination for the following reconstruction phase. Finally, a curriculum learning-based training scheme is further proposed to improve the convergence of the whole framework. Extensive experimental results on synthetic and real-world low-resolution images show that the proposed all-in-one collaboration framework not only produces favorable high-resolution results while removing serious degradation, but also has high computational efficiency, outperforming state-of-the-art methods. We also have applied ACF to some image-quality sensitive practical task, such as pose estimation, to improve estimation accuracy of low-resolution images.
Bi-manual Haptic-based Periodontal Simulation with Finger Support and Vibrotactile Feedback

The rise of virtual reality and haptic technologies has created exciting new applications in medical training and education. In a dental simulation, haptic technology can create the illusion of substances (teeth, gingiva, bone, etc.) by providing interaction forces within a simulated virtual world of the mouth. In this article, a haptic periodontal training simulation system, named Haptodont, is developed and evaluated for simulating periodontal probing. Thirty-two faculty members from New York University College of Dentistry were recruited and divided into three groups to evaluate three fundamental functionalities: Group 1 evaluated bi-manual 3 Degrees of Freedome (DoF) haptic interaction, Group 2 evaluated bi-manual 3 DoF haptic interaction with a finger support mechanism, and Group 3 evaluated bi-manual 3 DoF haptic interaction with finger support mechanism and vibrotactile feedback. The probe and mirror interactions were simulated with the Geomagic Touch haptic device whereas the finger support was implemented using the Novint Falcon device. The three groups conducted two probing tasks: healthy gingiva scenario with no pockets (2- to 3-mm depth) and periodontitis scenario with deep pockets (4- to 8-mm depth). Results demonstrated that experts performed comparably to clinical settings in terms of probing depth error (within 0.3 to 0.6 mm) and probing forces (less than 0.5 N). Furthermore, the finger support mechanism significantly improved the probing accuracy for periodontitis condition in the lingual region. The argument that probing the lingual region is more difficult than the buccal region is supported by quantitative evidence (significantly higher probing depth error and probing force). Further research is planned to improve the usability of the finger support, integrate the Haptodont system into the pre-clinical curriculum, and evaluate the Haptodont system with dental students as a learning tool.
New material of the frog Hungarobatrachus szukacsi Szentesi & Venczel, 2010, from the Santonian of Hungary, supports its neobatrachian affinities and reveals a Gondwanan influence on the European Late Cretaceous anuran fauna

ABSTRACT The Late Cretaceous anuran Hungarobatrachus szukacsi Szentesi & Venczel, 2010 was erected for isolated ilia and tibio-fibulae from the Santonian-age Iharkút locality, in northwestern Hungary. On the strength of ilial features, H. szukacsi was interpreted as a neobatrachian and possible ranoid, making it the only pre-Cenozoic occurrence for both clades in Laurasia. New ilia and the first examples of skull bones (incomplete frontoparietals, squamosals, maxillae, and angulosplenials) from the type locality provide new insights into the taxonomic distinctiveness, osteology, and evolutionary history of H. szukacsi. In addition to its diagnostic ilia (e.g., dorsal crest tall and ornamented laterally with prominent ridges; extensive interiliac tubercle developed across entire medial surface of acetabular region), H. szukacsi is characterized further by having a moderately hyperossified skull exhibiting such traits as frontoparietals, squamosals, and maxillae externally covered with prominent pit-and-ridge and weakly developed tuberculate ornament (i.e., exostosis), frontoparietals solidly fused along midline, frontoparietals expanded posterolaterally to form a broad squamosal process, squamosals expanded anteroposteriorly to form a plate-like lamella alaris, and maxilla articulating posteriorly with the quadratojugal to form a solid bony ‘cheek'. The first cladistic analysis to include H. szukacsi corroborates its neobatrachian status, but consistently places it among hyloids, rather than ranoids as originally proposed. Indications of hyloids on the African continent and in Madagascar during the Late Cretaceous, suggest that the ancestor of H. szukacsi may have dispersed from Africa, across the proto-Mediterranean and into Europe, prior to the Santonian.
Loss of stra8 Increases Germ Cell Apoptosis but Is Still Compatible With Sperm Production in Atlantic Salmon (Salmo salar)

Entering meiosis strictly depends on stimulated by retinoic acid 8 (Stra8) gene function in mammals. This gene is missing in a number of fish species, including medaka and zebrafish, but is present in the majority of fishes, including Atlantic salmon. Here, we have examined the effects of removing stra8 on male fertility in Atlantic salmon. As in mammals, stra8 expression was restricted to germ cells in the testis, transcript levels increased during the start of puberty, and decreased when blocking the production of retinoic acid. We targeted the salmon stra8 gene with two gRNAs one of these were highly effective and produced numerous mutations in stra8, which led to a loss of wild-type (WT) stra8 expression in F0 salmon testis. In maturing stra8 crispants, the spermatogenetic tubuli were partially disorganized and displayed a sevenfold increase in germ cell apoptosis, in particular among type B spermatogonia and spermatocytes. The production of spermatogenic cysts, on the other hand, increased in maturing stra8 crispants. Gene expression analysis revealed unchanged (lin28a, ret) or reduced levels (egr1, dusp4) of transcripts associated with undifferentiated spermatogonia. Decreased expression was recorded for some genes expressed in differentiating spermatogonia including dmrt1 and ccnd2 or in spermatocytes, such as ccna1. Different from Stra8-deficient mammals, a large number of germ cells completed spermatogenesis, sperm was produced and fertilization rates were similar in WT and crispant males. While loss of stra8 increased germ cell apoptosis during salmon spermatogenesis, crispants compensated this cell loss by an elevated production of spermatogenic cysts, and were able to produce functional sperm. It appears that also in a fish species with a stra8 gene in the genome, the critical relevance this gene has attained for mammalian spermatogenesis is not yet given, although detrimental effects of the loss of stra8 were clearly visible during maturation.
Two-Phase Lineage Specification of Telencephalon Progenitors Generated From Mouse Embryonic Stem Cells

Proper brain development requires precisely controlled phases of stem cell proliferation, lineage specification, differentiation, and migration. Lineage specification depends partly on concentration gradients of chemical cues called morphogens. However, the rostral brain (telencephalon) expands prominently during embryonic development, dynamically altering local morphogen concentrations, and telencephalic subregional properties develop with a time lag. Here, we investigated how progenitor specification occurs under these spatiotemporally changing conditions using a three-dimensional in vitro differentiation model. We verified the critical contributions of three signaling factors for the lineage specification of subregional tissues in the telencephalon, ventralizing sonic hedgehog (Shh) and dorsalizing bone morphogenetic proteins (BMPs) and WNT proteins (WNTs). We observed that a short-lasting signal is sufficient to induce subregional progenitors and that the timing of signal exposure for efficient induction is specific to each lineage. Furthermore, early and late progenitors possess different Shh signal response capacities. This study reveals a novel developmental mechanism for telencephalon patterning that relies on the interplay of dose- and time-dependent signaling, including a time lag for specification and a temporal shift in cellular Shh sensitivity. This delayed fate choice through two-phase specification allows tissues with marked size expansion, such as the telencephalon, to compensate for the changing dynamics of morphogen signals.
Morphological characterization and genotypic identity of African yam bean (Sphenostylis stenocarpa Hochst ex. A. Rich. Harms) germplasm from diverse ecological zones

Abstract African yam bean (AYB) is an affordable protein source capable of diversifying the food base in sub-Saharan Africa. However, research efforts made towards the crop's improvement and in expanding production are limited. This study characterized 169 AYB accessions at Jimma, Ethiopia, using 31 phenotypic characters. The analysis of variance revealed highly significant (P < 0.01) differences for days to 50% flowering, days to first flowering, leaf area, number of seeds per pod, pod length, seed thickness, total seed weight, petiole length and significant (P < 0.05) difference for terminal leaf length. Accession TSs62B produced the highest number of seeds per pod (17.65) and recorded the highest 100 seed weight (25.30 g), while 3A was the earliest to flower at an average of 84.50 d. Principal component analysis (PCA) of qualitative traits attributed 77.6% of observed variations to the first five principal components, of which the first two PC axes accounted for 53.6% of total variations. Cluster analysis and PCA biplot distinctly grouped the accessions into two major groups, cluster I had the highest number of accessions (108). The analytical approaches used confirmed considerable diversity across the germplasm with a distance matrix ranging from 0.37 to 0.85. The extent of diversity reflected in the current study provides breeders the baseline information to design breeding strategies, which might help identify materials for release as variety or parental lines for hybridization programmes.
Understanding surrogate measures of overall survival after trans‐arterial chemoembolization of hepatocellular carcinoma

Trans- arterial chemoembolization (TACE) is the most common treatment adopted for patients with hepatocellular carcinoma (HCC) 1,2 . It is known that TACE candidates, most belonging to the intermediate Barcelona Clinic Liver Cancer (BCLC) stage, present highly heteroge-neous clinical features, which determine a wide range of observed survivals, challenging the estimation of the health benefit both in randomized controlled trials (RCTs) and in the real- world practice. 2,3 In the study from Celsa and colleagues, a systematic search of studies including HCC patients treated with TACE, reporting both overall survival (OS) and time- to- progression (TTP) or progression- free survival (PFS), was performed to assess whether TTP of PFS can be considered as good surrogate measures of OS. 4 The need for such study comes from widespread use of TTP and PFS as surrogate outcome measures for OS in the treatment of HCC. In oncological trials, OS remains the gold standard to assess the treatment- related clinical benefit. 5 However, OS assessment requires large sample size and it is time- and cost- consuming so that surrogate radiology- based endpoints, such as PFS and TTP are commonly used to overcome these limitations. In addition, PFS and TTP are employed to early assess the antitumour treatment efficacy since they are not influenced by post- progression survival and by the effect of post- progression therapies. 6 However, prior to the use of surrogate endpoints in TACE studies, validation is required to eval-uate its robustness and a formal appraisal was never provided until the work of Celsa and colleagues. 4 The methodology reported is complex and for sake of clarity we need to briefly summarize the approach. Authors extracted data from 13 studies (7 RCTs 6 observational
A competitive direct enzyme-linked immunosorbent assay for the rapid detection of deoxynivalenol: development and application in agricultural products and feedstuff

ABSTRACT A competitive direct enzyme-linked immunosorbent assay (cd-ELISA) was developed for the rapid detection of deoxynivalenol (DON) in food and feedstuff. Polyclonal antibodies against DON were generated by immunizing rabbits with 3-HS-DON-BSA conjugates. In this assay, the sensitivity (measured as IC50) and limit of detection (measured as IC15) were 0.03 and 0.003 mg kg−1, respectively. A total of eight sample types (barley, wheat, oat, maize, rice, flour, milk and feedstuff) were chosen to evaluate the cd-ELISA assay performance. The sample could be directly detected after extraction and dilution with double-distilled water. The limit of detection in the samples was in the range of 0.15–0.48 mg kg−1. In the end, the spike and recovery results in both cd-ELISA and high-performance liquid chromatography (HPLC) were compared for assay validation. The recovery results ranged between 70% and 100%. A good correlation (R2 = 0.9613) between ELISA and HPLC was obtained.
Synthesis and Characterization of Single Crystalline Metal Nitride Fluorides

There were two primary objectives for this thesis work, both of which are focused on inorganic nitride-fluoride (N-F) chemistry. The first objective was to prepare both previously known and new M2NF compounds in order to further elucidate the crystal chemistry of known phases, as well as to explore synthesis routes for new mixed metal compounds. The synthesis approach in all cases involved first preparing AMF3 (A = NH4 or K+; M = Cu, Mg, Co) perovskite-type fluorides as precursors. Modifications of known synthesis methods for these compounds led to very pure, dry precursor materials. Doubled cubic Ca2NF crystals prepared from a KCuF3 precursor were analyzed via high resolution X-ray diffraction, from which it was learned that Frenkel defects thought to be present are actually a non-stoichiometric defect. The second goal of this project was to synthesize new mixed metal nitride fluoride materials. Only two such materials have been reported in the literature, and one of these is a fluorine insertion compound. The most significant result from this part of the project was the successful preparation of a CaMgNF phase related to rocksalt, but with quadrupled unit cell parameters due to ordering of cations and anions along the cell edges. This is the first bimetallic nitride-fluoride to be prepared that is a direct analog of
A Systems Approach to Examining PhD Students' Well-Being: An Australian Case

Previous research regarding PhD students’ well-being (PhD-WB) has lacked a comprehensive and systemic analysis. This research engages with a systems approach to examine the multiple variables, including feedback mechanisms, which influence PhD-WB over time. The model was developed using a structural analysis method (Cross-impact analysis MICMAC) that informed a causal loop diagram (CLD). The aim was to understand what promotes (drivers) and inhibits (barriers) PhD students’ well-being. The results show that PhD students’ well-being reflects an interplay between university, financial support, students’ mental and physical health, and family/friends. However, the analysis shows that the role of the drivers is dynamic, and they can become barriers in certain circumstances. This insight validates the application of systems thinking to illustrate the complexity of PhD students’ well-being.
Students Perceptions, System Characteristics and Online Learning During the COVID-19 Epidemic School Disruption

Due to the emergency educational consequences of the COVID-19 epidemic, it is necessary to find an effective and alternative way of learning. Moreover, during this epidemic, the Chinese Ministry of Education announced the “Disrupted Classes, Undisrupted Learning” initiative, offering flexible online learning. With the aim of facilitating a sound learning environment when using online learning systems, various kinds of tools can be applied. Tencent Meeting is one tool that offers various learning features. This study aimed to investigate how students perceived the effect of the Tencent Meeting system features on the two main determinants of the TAM model, namely perceived ease of use (PEOU) and perceived usefulness (PU). The study further analyzed the effects of these two determinants on learning performance. Data were analyzed using regression analysis. The study found the Tencent Meeting system features could account for 55.1% of PEOU and 40% of PU. Another finding shows that PEOU and PU had a significant effect on the students' learning performance. Finally, a discussions and implications are presented.