Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparable Performance of Deep Learning–Based to Manual-Based Tumor Segmentation in KRAS/NRAS/BRAF Mutation Prediction With MR-Based Radiomics in Rectal Cancer

Radiomic features extracted from segmented tumor regions have shown great power in gene mutation prediction, while deep learning–based (DL-based) segmentation helps to address the inherent limitations of manual segmentation. We therefore investigated whether deep learning–based segmentation is feasible in predicting KRAS/NRAS/BRAF mutations of rectal cancer using MR-based radiomics. In this study, we proposed DL-based segmentation models with 3D V-net architecture. One hundred and eight patients’ images (T2WI and DWI) were collected for training, and another 94 patients’ images were collected for validation. We evaluated the DL-based segmentation manner and compared it with the manual-based segmentation manner through comparing the gene prediction performance of six radiomics-based models on the test set. The performance of the DL-based segmentation was evaluated by Dice coefficients, which are 0.878 ± 0.214 and 0.955 ± 0.055 for T2WI and DWI, respectively. The performance of the radiomics-based model in gene prediction based on DL-segmented VOI was evaluated by AUCs (0.714 for T2WI, 0.816 for DWI, and 0.887 for T2WI+DWI), which were comparable to that of corresponding manual-based VOI (0.637 for T2WI, P=0.188; 0.872 for DWI, P=0.181; and 0.906 for T2WI+DWI, P=0.676). The results showed that 3D V-Net architecture could conduct reliable rectal cancer segmentation on T2WI and DWI images. All-relevant radiomics-based models presented similar performances in KRAS/NRAS/BRAF prediction between the two segmentation manners.
RNA Sequencing Reveals Dynamic Carbohydrate Metabolism and Phytohormone Signaling Accompanying Post-mowing Regeneration of Forage Winter Wheat (Triticum aestivum L.)

Winter wheat (Triticum aestivum L.) is used as fresh green winter forage worldwide, and its ability to regenerate after mowing determines whether it can be used for forage production; however, the molecular mechanism of regeneration is poorly understood. This study identified long-chain coding and non-coding RNAs in the wheat cultivar “XN9106,” which is cultivated for forage and grain production separately in winter and summer, and analyzed their function during post-mowing regeneration. The results showed that the degradation of carbohydrate plays an important role in regeneration, as demonstrated by decreased carbohydrate content. The increased gene expression of enzymes including β-amylase, β-fructofuranosidase, sucrose synthase, sucrose-6-phosphate synthase, trehalose-6-phosphate synthase, and trehalose-6-phosphate phosphatase in mowed seedlings suggests regeneration is fueled by degraded carbohydrates that provide energy and carbon skeletons for the Krebs cycle and amino acid synthesis. The decreased auxin content relieved the inhibition of cytokinin synthesis, that controls the transition from cell division to cell expansion and stimulates cell expansion and differentiation during the cell expansion phase, and eventually accelerate post-mowing regeneration of seedlings. Additionally, differentially expressed long-chain non-coding RNAs (lncRNAs) might participate in the regulation of gene expression related to carbohydrate metabolism and hormone signal transduction. This study demonstrated the responses of key mRNAs and lncRNAs during post-mowing regeneration of winter wheat and revealed the importance of carbohydrate and hormone during regeneration, providing valuable information for genetic improvement of forage wheat.
Characterization of intracellular calcium stores in the exocrine pancreas

Isolated rabbit pancreatic acinar cells, permeabilized by saponin treatment and incubated in the presence of 0.1 μΜ free Ca, accumulated 3.3 nmol of Ca/mg of acinar protein in an energy-dependent pool. Part of this energy-dependent pool could be released by GTP in a polyethylene glycol-dependent manner. The kinetics of GTP-lnduced release of Ca* showed a blphasic pattern with an initial rapid phase followed by a sustained slower phase. In contrast, ІРз-induced release of Ca was completed within 30 s following addition of IP3. No reuptake of Ca was observed following GTPor ІРз-induced release of 2+ ,2+ Ca . The GTP effect was independent of IP3 and not inhibited by Ca , indicating that the ІРз-operated Ca channel is not involved in GTP-induced release of Ca. The size of the ІРз-releasable pool was not affected by GTP, indicating that GTP, when added to permeabilized acinar cells, does not promote the coupling between ІРз-insensitive and ІРз-sensitive Ca accumulating organelles. Thus, in permeabilized acinar ceils, GTP and IP3 act on different Ca* sequestering pools. Interestingly, however, comparison of the size of the GTP-releasable pool with that of the ІРэ-releasable pool for the cell preparations used In the present study, revealed an I η versed relationship, indicating that at the time of permeabilization the GTP-releasable pool can be coupled to a greater or lesser extent to the ІРз-releasable pool. This suggests that, in the intact cell, a GTP-dependent mechanism may exist that controls the size of the ІРз-releasable pool by coupling ІРз-lnsensitive to ІРз-sensitive organelles. Moreover, this suggests that the extent of coupling Is preserved during permeabilization. Pancreatic secretogogues such as acetylcholine and cholecystokinin stimulate digestive enzyme secretion by activating a pbosphatidyLmositol 4,5-bispbospbale-specific phosphodiesterase Abbreviations used IPs, inositol 1,4,5 triphosphate PEG, polyethylene glycol HEEDTA, N-(2-hydroxyethyl) ethylenediamine-N,N'. N' biacche acid and HEPES, 4-(2-hydroxyethyl) 1 piperazme elhanesulfonic acid catalyzing the formation of the intracellular messengers 1,2-diacylgIycerol [1, 2] and inositol 1,4,5-tnsphospbate [2]. A second messenger role for inositol 1,4,5-tnspbosphate (ІРз) was proposed for the first time by Streb et al. [3]. Using permeabilized pancreatic acinar cells, they showed that ГРз rapidly released Ca from an energy-dependent vesicular store Io subsequent subfractionation studies, this ГРз-releasable Ca
Groundwater, Soil, and Vegetation Interactions at Discrete Riparian Inflow Points (DRIPs) and Implications for Boreal Streams

Hydrological processes at hillslope and catchment scales explain a large part of stream chemistry dynamics through source-transport mechanisms from terrestrial to aquatic ecosystems. Riparian zones play a central role, as they exert a strong influence on the chemical signature of groundwater discharge to streams. Especially important are riparian areas where upslope subsurface flow paths converge, because they connect a large part of the catchment to a narrow section of the stream. Recent research shows that both in terrestrial and aquatic ecosystems, riparian convergence zones fulfill important biogeochemical functions that differ from surrounding riparian zones. Most catchment-scale conceptual frameworks focus on generalized hillslope-riparian-stream transects and do not explicitly consider riparian convergence zones. This study integrates collective work on hydrology, groundwater chemistry, vegetation and soils of discrete riparian inflow points (DRIPs) in a boreal landscape. We show that compared to adjacent riparian forests, DRIPs have groundwater levels that are consistently near the surface, and supply organic-rich water to streams. We suggest that interactions between hydrology, wetland vegetation, and peat soil development that occur in DRIPs leads to their unique groundwater chemistry and runoff dynamics. Stream-based studies show that across flow conditions, groundwater inputs from DRIPs to headwater reaches influence stream temperature, water chemistry and biology. As such, accounting for DRIPs can complement existing hillslope and stream observations, which would allow better representation of chemical and biological interactions associated with convergence of subsurface flow paths in riparian zones.
Single-Cell RNA Sequencing of Retina:New Looks for Gene Marker and Old Diseases

The retina is composed of 11 types of cells, including neurons, glial cells and vascular bed cells. It contains five types of neurons, each with specific physiological, morphological, and molecular definitions. Currently, single-cell RNA sequencing (sRNA-seq) is emerging as one of the most powerful tools to reveal the complexity of the retina. The continuous discovery of retina-related gene targets plays an important role in helping us understand the nature of diseases. The revelation of new cell subpopulations can focus the occurrence and development of diseases on specific biological activities of specific cells. In addition, sRNA-seq performs high-throughput sequencing analysis of epigenetics, transcriptome and genome at the single-cell level, with the advantages of high-throughput and high-resolution. In this paper, we systematically review the development history of sRNA-seq technology, and summarize the new subtypes of retinal cells and some specific gene markers discovered by this technology. The progress in the diagnosis of retinal related diseases is also discussed.
Taxonomy and Molecular Phylogeny of Two New Urostylid Ciliates (Protozoa: Ciliophora) From Chinese Wetlands and Establishment of a New Genus

Hypotrich ciliates with evolutionary novelties are continually being discovered, challenging the current taxonomic system and attracting increased attention. In the present work, two new urostylid ciliates, Heterobakuella bergeri gen. nov., sp. nov. and Anteholosticha perezuzae sp. nov., isolated from Chinese wetland samples, were identified based on morphology and 18S rRNA gene sequences. Heterobakuella gen. nov. is defined by three frontal cirri, single buccal cirrus, one parabuccal cirrus, midventral complex composed of cirral pairs and one cirral row, one left and two right marginal cirral rows, transverse and pretransverse cirri present, caudal and frontoterminal cirri absent. Heterobakuella can be easily distinguished from the morphologically most similar genus, Apobakuella, mainly by the single buccal cirrus (vs. one buccal cirral row) and one parabuccal cirrus (vs. several parabuccal cirral rows originated from different anlagen). Phylogenetic analyses show that H. bergeri branches within the clade formed by Bergeriella ovata, Monocoronella carnea, Anteholosticha gracilis, and Neourostylopsis spp. , rather than the clade represented by Apobakuella. The other species, A. perezuzae, is mainly characterized by a distinctly slender body shape with an average length:width ratio about 7, distinctively shaped biconcave and greenish cortical granules, as well as one or two pretransverse cirri. Phylogenetic analyses indicate the genus Anteholosticha is non-monophyletic.
Early Serum Infliximab Levels in Pediatric Ulcerative Colitis

Background: Data on serum infliximab concentrations during induction in pediatric ulcerative colitis are limited. The study aim is to evaluate the relationship between serum infliximab concentrations during induction and short-term clinical remission in children with ulcerative colitis. Methods: We carried out a prospective, multi-center cohort study in pediatric patients with ulcerative colitis. Serum infliximab concentrations were collected at peak dose #1, week 1, trough pre-dose #2, and trough pre-dose #3. Infliximab dosing was left to investigator discretion. Clinical remission was defined by pediatric ulcerative colitis activity index <10 at week 8. Results: Twenty-four of thirty-four subjects (71%) achieved clinical remission at week 8. The median infliximab concentrations were 33.0 μg/mL (interquartile range: 26.5–52.1 μg/mL) pre-dose #2 and 22.5 μg/mL (interquartile range:15.9–32.3 μg/mL) pre-dose #3. Trough pre-dose #2 infliximab concentration yielded area under receiver operator characteristic curve 0.7, 95% CI: 0.5–0.9 in predicting week 8 clinical remission; a cut-off of 33.0 μg/mL yielded 62.5% sensitivity, 66.7% specificity. Trough pre-dose #3 infliximab concentrations were lower for subjects <10 years compared to ≥ 10 years [median 15.9 μg/mL, interquartile range (IQR) 8.5–21.8 μg/mL vs. 27.7 μg/mL, IQR 17.2–46.7 μg/mL, p = 0.01] and correlated with baseline weight (Spearman's rank correlation coefficient 0.45, p = 0.01). The median half-life following first IFX dose was 6.04 days (IQR 5.3–7.9 days). Conclusions: Infliximab concentrations ≥33 μg/mL prior to the second dose were associated with week 8 clinical remission. As young age and low body weight impact infliximab concentration, prospective studies with proactive adjustment in pediatric patients with ulcerative colitis should be carried out. Clinicians caring for children with UC should diligently adjust and monitor infliximab to optimize response.
High-Intensity Intermittent Exercise Performed on the Sand Induces Higher Internal Load Demands in Soccer Players

This study aimed to examine the acute physiological effect of shuttle-run-based high-intensity intermittent exercise (HIIE) performed at the same relative speed (i. e., 100% PST−CAR) on sand (SAND) and grass (GRASS) in male junior soccer players. Seven Under-23 Brazilian national league (“Série A”) soccer players completed four testing sessions in either SAND or GRASS surface condition. The first two testing sessions consisted of performing a maximal progressive shuttle-run field protocol until volitional exhaustion (Carminatti's test, T-CAR), whereas the third and fourth sessions comprised a HIIE session on each ground surface. The HIIE session consisted of three 5-min bouts [12 s shuttle-run (with a direction change every 6 s)/12 s of passive rest] performed at 100% of T-CAR peak speed (PST−CAR) with 3 min of passive recovery between sets. Measurements of oxygen uptake (VO2), heart rate (HR), blood lactate concentration ([La]), and rating of perceived exertion (RPE) were performed during all conditions. The SAND condition elicited significantly higher %VO2peak (94.58 ± 2.73 vs. 87.45 ± 3.31%, p < 0.001, d = 2.35), %HRpeak (93.89 ± 2.63 vs. 90.31 ± 2.87%, p < 0.001, d = 1.30), RPE (8.00 ± 0.91 vs. 4.95 ± 1.23 a.u., p < 0.001, d = 2.82), and [La] (10.76 ± 2.37 vs. 5.48 ± 1.13 mmol/L, p < 0.010, d = 2.84). This study showed that higher internal workloads are experienced by the players during a single HIIE session performed on a softer surface as SAND, even when the exercise intensity was individualized based on 100%PST−CAR.
Variations in Rainfall Affect the Responses of Foliar Chemical Properties of Cunninghamia lanceolata Seedlings to Soil Warming

Climate warming is becoming an increasingly serious threat. Understanding plant stoichiometry changes under climate warming is crucial for predicting the effects of future warming on terrestrial ecosystem productivity. Nevertheless, how plant stoichiometry responds to warming when interannual rainfall variation is considered, remains poorly understood. We performed a field soil warming experiment (+5°C) using buried heating cables in subtropical areas of China from 2015 to 2018. Stoichiometric patterns of foliar C:N:P:K:Ca:Mg, non-structural carbohydrate, and stable isotope of Cunninghamia lanceolata seedlings were studied. Our results showed that soil warming decreased foliar P and K concentrations, C:Ca, P:Ca, and P:Mg ratios. However, soil warming increased foliar Ca concentration, δ15N value, C:P and N:P ratios. The response ratios of foliar N, C:N, and δ15N to soil warming were correlated with rainfall. Our findings indicate that there was non-homeostasis of N and C:N under warming conditions. Three possible reasons for this result are considered and include interannual variations in rainfall, increased loss of N, and N limitation in leaves. Piecewise structural equation models showed that stoichiometric non-homeostasis indirectly affected the growth of C. lanceolata seedlings in response to soil warming. Consequently, the growth of C. lanceolata seedlings remained unchanged under the warming treatment. Taken together, our results advance the understanding of how altered foliar stoichiometry relates to changes in plant growth in response to climate warming. Our results emphasize the importance of rainfall variations for modulating the responses of plant chemical properties to warming. This study provides a useful method for predicting the effects of climate warming on economically important timber species.
Physicians' Acceptance of Triage Guidelines in the Context of the COVID-19 Pandemic: A Qualitative Study

Aims: One of the major ethical challenges posed by the Covid-19 pandemic comes in the form of fair triage decisions for critically ill patients in situations where life-saving resources are limited. In Spring 2020, the Swiss Academy of Medical Sciences (SAMS) issued specific guidelines on triage for intensive-care treatment in the context of the Covid-19 pandemic. While evidence has shown that the capacities of intensive care medicine throughout Switzerland were sufficient to take care of all critically ill patients during the first wave of the outbreak, no evidence is available regarding the acceptance of these guidelines by ICU staff. The aim of this qualitative study was to explore the acceptance and perceived implementation of the SAMS guidelines among a sample of senior physicians involved in the care of Covid-19 patients in the Canton of Ticino. Specific objectives included capturing and describing physicians' attitudes toward the guidelines, any challenges experienced in their application, and any perceived factors that facilitated or would facilitate their application. Methods: We conducted face-to-face and telephone interviews with a purposive sample of nine senior physicians employed as either head of unity, deputy-head of unit, or medical director in either one of the two Covid-19 hospitals in the Canton of Ticino during the peak of the outbreak. Interviews were transcribed verbatim and thematically analyzed using an inductive approach. Results: We found that participants held different views regarding the nature of the guidelines, saw decisions on admission as a matter of collective responsibility, argued that decisions should be based on a medical futility principle rather than an age criterion, and found that difficulties to address end-of-life issues led to a comeback of paternalism. Conclusions: Results highlight the importance of clarifying the nature of the guidelines, establishing authority, and responsibility during triaging decisions, recognizing and addressing sources of interference with patients' autonomy, and the need of a cultural shift in timely and efficiently addressing end-of-life issues.
Contributions of Service-Learning to more inclusive and less gender-biased Physical Education: the views of Spanish Physical Education Teacher Education students

ABSTRACT There continue to be gender biases and masculinization within Physical Education (PE). Therefore, PE teacher training should challenge current curricular practices and promote transformative pedagogical approaches. We advocate service-learning (SL) which shares its essential principles and research outcomes with feminist pedagogy. This study aims to discover whether generic SL projects, aimed at meeting the needs of at-risk populations, might promote a non-gender-biased conception of PE in Physical Education Teacher Education (PETE) students/trainees. A qualitative hermeneutic-phenomenological method was used to explore the trainees’ personal experiences. Participants included 292 PETE trainees from Universities belonging to the Spanish Service-Learning Research Network in Physical Activity and Sport for Social Inclusion. PETE trainees experienced SL programmes aimed at promoting social inclusion of vulnerable populations through physical activity. A total of 292 reflection journals, 12 semi-structured interviews and 13 focus-groups were conducted. The findings were organized into four categories: ‘Equal footing’, ‘Overcoming masculinized views of PE’, ‘Beyond the class walls’, and ‘It seems that PE has evolved’. In conclusion, these findings show that SL might lead PETE trainees to see PE in a less gender-biased way and that a well-designed curriculum will be inclusive, empowering students who do not fit into the hegemonic expectations of masculinity.
The attributive adjective in Zimbabwean isiNdebele

This article discusses attributive adjectives in Zimbabwean isiNdebele. In traditional grammar, the attributive adjectives are treated as words whose function is to qualify a noun in a noun phrase. According to this analysis, an attributive adjective has the structure: adjective concord (a relative marker a- + a noun class prefix) and an adjective stem. However, there are instances where the attributive function is expressed by a construction that is larger than a word. In these constructions, the relative marker and the noun class prefix may be separated by a subject marker, negation marker, aspect markers, tense markers, inchoactive/auxiliary verbs, or a subject of the relative clause. I present an alternative analysis, according to which the attributive adjectival function is expressed by a relative clause rather than by an adjectival word category. I maintain that adjectival roots in isiNdebele are derived from class neutral roots by merging with an adjectiviser head (adj), and that the function of an adjective is to complement auxiliary verbs and inchoactive verbs in a predicate. I suggest that the relative operator is base generated as a complement of an adjective in an adjective phrase and then moves to spec C via spec in spec Pr and spec T respectively. The C-head a- then affixes to the subject of the relative clause in the formation of strategy 2 relatives and it affixes to T in the formation of strategy 1 relatives.
From face-to-face to flipped: strategic adaptation of library instruction during a pandemic

Abstract When the COVID-19 pandemic forced universities in China to abruptly transition to virtual instruction, library services adapted quickly to provide research services, instruction, and access to collections. The library at NYU Shanghai was about to begin its sixth year of providing library research workshops to Freshmen enrolled in foundational courses, and was challenged to quickly revise a familiar and successful information literacy program to meet the demands of this new fully-online environment. This paper details how the library used a SWOT Analysis to guide the decision-making process behind this transition. It then describes the resulting instruction program, which adopts a flipped classroom approach that incorporates online video modules, assessment tools, and a variety of synchronous and asynchronous instructional followup sessions.
Center for Embedded Computer Systems University of California , Irvine Specification and Design of a MP 3 Audio Decoder

In an effort to understand, experience and prove the benefits of automated SoC design, this report describes the specification modeling, design space exploration and implementation of a real world example using SpecC based System on Chip Environment (SCE). The report covers a complete description of developing the specification model of a MPEG-1 Layer 3 (MP3) audio decoder in SpecC language and the subsequent design space exploration and implementation using SCE. This report also attempts to improve the SoC design process by identifying the tasks in specification modeling that can be automated.