Miracle-dz/UniFAR-FTUs huggingface dataset:
Hospitalized cancer patients with comorbidities and low lymphocyte counts had poor clinical outcomes to immune checkpoint inhibitors

Background Immune checkpoint inhibitor (ICI) therapy has improved survivals with a favorable toxicity profile in a variety of cancer patients. We hypothesized that hospitalized cancer patients who have acute or chronic comorbidities may have suppressed immune systems and poor clinical outcomes to ICIs. The objective of this study was to explore clinical outcomes and predictive factors of hospitalized cancer patients who received ICI therapy at an NCI-designated Comprehensive Cancer Center. Methods A retrospective review of electronic medical records was conducted for adult cancer patients who received an FDA-approved ICI during admission from 08/2016 to 01/2022. For each patient we extracted demographics, cancer histology, comorbidities, reasons for hospitalization, ICI administered, time from treatment to discharge, time from treatment to progression or death, and complete blood counts. Progression-free survival (PFS) and overall survival (OS) were estimated using the Kaplan–Meier method and compared using the log-rank test. The 95% confidence interval for survival was calculated using the exact binomial distribution. Statistical significance was defined as 2-sided p<0.05. Results Of 37 patients identified, 2 were excluded due to lack of complete blood counts on admission. Average hospital stay was 24.2 (95% CI 16.5, 31.9) days. Ten (27.0%) patients died during the same hospitalization as treatment. Of those who followed up, 22 (59.5%) died within 90 days of inpatient therapy. The median PFS was 0.86 (95% CI 0.43, 1.74) months and median OS was 1.55 (95% CI 0.76, 3.72) months. Patients with ≥3 comorbidities had poorer PFS (2.4 vs. 0.4 months; p=0.0029) and OS (5.5 vs. 0.6 months; p=0.0006). Pre-treatment absolute lymphocyte counts (ALC) <600 cells/µL were associated with poor PFS (0.33 vs. 1.35 months; p=0.0053) and poor OS (0.33 vs. 2.34 months; p=0.0236). Pre-treatment derived neutrophil to lymphocyte ratio (dNLR) <4 was associated with good median PFS (1.6 vs. 0.4 months; p=0.0157) and OS (2.8 vs. 0.9 months; p=0.0375). Conclusions Administration of ICI therapy was associated with poor clinical outcomes and high rates of both inpatient mortality and 90-day mortality after inpatient ICI therapy. The presence of ≥3 comorbidities, ALC <600/μL, or dNLR >4 in hospitalized patients was associated with poor survival outcomes.
Abscisic acid: Metabolism, transport, crosstalk with other plant growth regulators, and its role in heavy metal stress mitigation

Heavy metal (HM) stress is threatening agricultural crops, ecological systems, and human health worldwide. HM toxicity adversely affects plant growth, physiological processes, and crop productivity by disturbing cellular ionic balance, metabolic balance, cell membrane integrity, and protein and enzyme activities. Plants under HM stress intrinsically develop mechanisms to counter the adversities of HM but not prevent them. However, the exogenous application of abscisic acid (ABA) is a strategy for boosting the tolerance capacity of plants against HM toxicity by improving osmolyte accumulation and antioxidant machinery. ABA is an essential plant growth regulator that modulates various plant growth and metabolic processes, including seed development and germination, vegetative growth, stomatal regulation, flowering, and leaf senescence under diverse environmental conditions. This review summarizes ABA biosynthesis, signaling, transport, and catabolism in plant tissues and the adverse effects of HM stress on crop plants. Moreover, we describe the role of ABA in mitigating HM stress and elucidating the interplay of ABA with other plant growth regulators.
Flexible and high quality plant growth prediction with limited data

Predicting plant growth is a fundamental challenge that can be employed to analyze plants and further make decisions to have healthy plants with high yields. Deep learning has recently been showing its potential to address this challenge in recent years, however, there are still two issues. First, image-based plant growth prediction is currently taken either from time series or image generation viewpoints, resulting in a flexible learning framework and clear predictions, respectively. Second, deep learning-based algorithms are notorious to require a large-scale dataset to obtain a competing performance but collecting enough data is time-consuming and expensive. To address the issues, we consider the plant growth prediction from both viewpoints with two new time-series data augmentation algorithms. To be more specific, we raise a new framework with a length-changeable time-series processing unit to generate images flexibly. A generative adversarial loss is utilized to optimize our model to obtain high-quality images. Furthermore, we first recognize three key points to perform time-series data augmentation and then put forward T-Mixup and T-Copy-Paste. T-Mixup fuses images from a different time pixel-wise while T-Copy-Paste makes new time-series images with a different background by reusing individual leaves extracted from the existing dataset. We perform our method in a public dataset and achieve superior results, such as the generated RGB images and instance masks securing an average PSNR of 27.53 and 27.62, respectively, compared to the previously best 26.55 and 26.92.
Adaptive biomineralization in two morphotypes of Sternaspidae (Annelida) from the Northern China Seas

Polychaetes are segmented annelid worms that play a key role in biomineralization in modern oceans. However, little is known about the underlying processes and evolutionary mechanisms. The ventro-caudal shield of Sternaspidae is a typical phosphate biomineral in annelids. Here, we investigated two sternaspids from the northern China Seas, Sternaspis chinensis and Sternaspis liui syn. n, which evolved diverse shield characteristics as local adaptation. Genetic distances, phylogenetic analyses of nuclear markers (18S and 28S genes), and mitochondrial genomes revealed that the latter is a junior synonym of the former. The integration of elemental composition and the transcriptomic analysis provided insights into phenotypic shield differences. The electron probe microanalysis showed that shields in S. chinensis were more biomineralized (i.e., with higher iron, phosphorus, and calcium contents) than those in S. liui syn. n. Transcriptomes of the body wall around shields determined 17,751 differentially expressed genes (DEGs) in two morphotypes of the synonymous species. Function enrichment analysis of DEGs showed that S. chinensis has an enrichment of the putative biomineralization pathways (i.e., ion transport and calmodulin binding), while S. liui syn. n consumed more energy and produced more proteins (i.e., oxidative phosphorylation and ribosome). DEGs allowed to identify seven shell matrix proteins expressed differentially in the two morphotypes, especially calponin, filamin, chitinase, and protease inhibitor BPTI/kunitz, which might contribute to shield evolutionary plasticity response to their living habitats. Overall, this study 1) revealed an environmental biomineralization adaptation in two polychaete morphotypes of one species by integrating shield chemical composition of shields and transcriptome analyses and 2) provided insights into the molecular mechanisms underlying polychaete biomineralization.
Utilizing mast cells in a positive manner to overcome inflammatory and allergic diseases

Mast cells (MCs) are immune cells widely distributed in the body, accompanied by diverse phenotypes and functions. Committed mast cell precursors (MCPs) leave the bone marrow and enter the blood circulation, homing to peripheral sites under the control of various molecules from different microenvironments, where they eventually differentiate and mature. Partly attributable to the unique maturation mechanism, MCs display high functional heterogeneity and potentially plastic phenotypes. High plasticity also means that MCs can exhibit different subtypes to cope with different microenvironments, which we call “the peripheral immune education system”. Under the peripheral immune education system, MCs showed a new character from previous cognition in some cases, namely regulation of allergy and inflammation. In this review, we focus on the mucosal tissues, such as the gastrointestinal tract, to gain insights into the mechanism underlying the migration of MCs to the gut or other organs and their heterogeneity, which is driven by different microenvironments. In particular, the immunosuppressive properties of MCs let us consider that positively utilizing MCs may be a new way to overcome inflammatory and allergic disorders.
Effect of SIRT1 on white matter neural network in adolescent patients with depression

Background This study aimed to explore the correlation between the rs12415800 polymorphism of the silent information regulator 1 (SIRT1) gene and the white matter neural circuit in adolescent patients with depression. Methods We enrolled 119 participants, comprising 59 adolescent patients with depression and 60 matched healthy controls for analysis. Patients were further subdivided based on genotype; GG, AG, and AA, with G representing the wild type gene, and A representing the A allele at rs12415800. Results We found that: (1) lower anisotropy fraction (FA) values in the left cingulate fasciculus and left anterior thalamus radiation in the AG/AA genotype were more likely to be affected by depression. (2) The FA values of the right inferior occipital-frontal fasciculus, right corticospinal tract, right inferior longitudinal fasciculus, and right superior longitudinal fasciculus regions in the depression (AG/AA) group were lower than in the depression (GG) group. (3) FA values of the right inferior occipital-frontal fasciculus left corticospinal tract, right inferior longitudinal fasciculus, left anterior thalamus radiation, right superior longitudinal fasciculus, left inferior longitudinal fasciculus, left uncinate fasciculus, and right anterior thalamus radiation in the depression (GG) group were lower than the control (GG) group. Conclusions The polymorphism locus of the SIRT1 gene rs12415800 may be related to changes in the microstructure of white matter fiber tracts, and patients carrying the A allele (AG/AA) have more changes in the white matter than those with the non-A allele (GG).
Deaf and non-deaf basketball and volleyball players' multi-faceted difference on repeated counter movement jump performances: Height, force and acceleration

The aim of this study was to compare the performances of Repetitive Counter Movement Jumping (basketball/volleyball) of deaf/non-deaf athletes. Athletes playing in the Turkish Deaf Basketball and Volleyball national teams and in Basketball and Volleyball First Leagues participated in the study. The study group consisted of 51 male athletes, including deaf basketball (n = 11; age: 26.18 ± 4.79 years), deaf volleyball (n = 12, age: 26.33 ± 4.27 years), non-deaf basketball (n = 14, age: 26.93 ± 4.87 years), and non-deaf volleyball (n = 14, age: 24.93 ± 5.10 years) players. As a result of the test, Jump Height from Take Off Velocity, Jump Height from Take Off Velocity, Jump Height from Flight Time, Counter Movement Acceleration, Push Off Acceleration, Average Velocity, Average Power, and Average Force were analyzed. Differences in the jump performances among the groups (deaf basketball and volleyball, non-deaf basketball, and volleyball) were tested by one-way analyses of variance (ANOVA) with Tukey's post-hoc follow-up testing when necessary for jump test. As a result, this is the first study to investigate the number of jumps and jump height, the force produced, acceleration at the time of jump, and jump velocity during 30 s in deaf and non-deaf basketball and volleyball players within the scope of individual Repeated Counter Movement Jump test. Based on the biomechanical changes according to our results, our findings show a greater decrease in the number of jumps and jump heights, the force produced, the acceleration at the moment of the jump and the jump velocity in all athletes, especially those that affect the deaf.
Vision Science : Photons to Phenomenology

This book revolutionizes how vision can be taught to undergraduate and graduate students in cognitive science, psychology, and optometry. It is the first comprehensive textbook on vision to reflect the integrated computational approach of modern research scientists. This new interdisciplinary approach, called "vision science," integrates psychological, computational, and neuroscientific perspectives. The book covers all major topics related to vision, from early neural processing of image structure in the retina to high-level visual attention, memory, imagery, and awareness. The presentation throughout is theoretically sophisticated yet requires minimal knowledge of mathematics. There is also an extensive glossary, as well as appendices on psychophysical methods, connectionist modeling, and color technology. The book will serve not only as a comprehensive textbook on vision, but also as a valuable reference for researchers in cognitive science, psychology, neuroscience, computer science, optometry, and philosophy.
Cultivation of Ulva fenestrata using herring production process waters increases biomass yield and protein content

Ulva spp. (sea lettuce) has recently gained attention as a sustainable protein source due to its high productivity and many nutritional properties interesting for the food industry. In this study, we explored a possible industrial symbiosis between herring production processing industries and Ulva fenestrata cultivation. We show that U. fenestrata cultivated in herring production process waters had four to six times higher biomass yields (27.17 - 37.07 g fresh weight vs. 6.18 g fresh weight) and three times higher crude protein content (> 30% dry weight vs. 10% dry weight) compared to U. fenestrata cultivated in seawater. Along with the elevation of protein, the herring production process waters also significantly increased levels of all essential amino acids in the seaweed biomass. The content of some heavy metals (arsenic, mercury, lead, and cadmium) was well below the maximum allowed levels in foodstuff. Therefore, quantities of biomass around 100 g dry weight could be consumed daily following the US Environmental Protection Agency’s reference doses. Combined, the results show that cultivation of U. fenestrata in herring production process waters has great potential to produce sustainable proteins for the growing world population. At the same time, nutrients of currently discarded process waters are circulated back to the food chain.
Spatial- and temporal-interpolations for efficient hybrid wave numerical simulations

The hybrid simulation method is developed for simulating wave propagation only in a localized heterogeneous media with hybrid inputs obtained once for all from a known reference model. Despite the fact that the hybrid simulation method has a wide range of applications in computational seismology, the associated error control of this method has received relatively little attention in previous research works. We quantitatively discuss the error of the two-step hybrid method in acoustic wave cases and propose a spatial refinement scheme to compute hybrid inputs based on the multi-elements spline interpolation, which is preferable to traditional Lagrange interpolation since it uses more polydirectional interpolated points. This method can also be used for local refinement of wavefield in more general applications, such as saving smooth wavefield in the full-waveform inversion framework. Furthermore, to save memory requirements, hybrid inputs are proposed to be sparsely stored with a high upsampling ratio during the global simulation, and the Fourier interpolation method is introduced to recover them to their original time series. To demonstrate the effect of the proposed methods, we perform several 2D and 3D hybrid wave numerical simulations using the spectral element method. We find that when the global and local meshing differs, the proposed spatial interpolation method can appreciably reduce the error of the hybrid waveforms caused by inaccurate hybrid inputs. We also point out that the Fourier interpolation can efficiently recover the original waveform, allowing hybrid inputs to be stored with time steps toward the Nyquist limit. Our method is expected to become a standard method to reduce the error of hybrid waveforms and save the memory requirements during hybrid simulations and has potential implications for further improving the accuracy of the so-called box tomography.
A survey of protein interactions and posttranslational modifications that influence the polyglutamine diseases

The presence and aggregation of misfolded proteins has deleterious effects in the nervous system. Among the various diseases caused by misfolded proteins is the family of the polyglutamine (polyQ) disorders. This family comprises nine members, all stemming from the same mutation—the abnormal elongation of a polyQ repeat in nine different proteins—which causes protein misfolding and aggregation, cellular dysfunction and disease. While it is the same type of mutation that causes them, each disease is distinct: it is influenced by regions and domains that surround the polyQ repeat; by proteins with which they interact; and by posttranslational modifications they receive. Here, we overview the role of non-polyQ regions that control the pathogenicity of the expanded polyQ repeat. We begin by introducing each polyQ disease, the genes affected, and the symptoms experienced by patients. Subsequently, we provide a survey of protein-protein interactions and posttranslational modifications that regulate polyQ toxicity. We conclude by discussing shared processes and pathways that bring some of the polyQ diseases together and may serve as common therapeutic entry points for this family of incurable disorders.
Enabling factor for cancer hallmark acquisition: Small nucleolar RNA host gene 17

The role of long non-coding RNA (lncRNA) in human tumors has gradually received increasing attention in recent years. Particularly, the different functions of lncRNAs in different subcellular localizations have been widely investigated. The upregulation of lncRNA small nucleolar RNA host gene 17 (SNHG17) has been observed in various human tumors. Growing evidence has proved that SNHG17 plays a tumor-promoting role in tumorigenesis and development. This paper describes the molecular mechanisms by which SNHG17 contributes to tumor formation and development. The different functions of SNHG17 in various subcellular localizations are also emphasized: its function in the cytoplasm as a competing endogenous RNA (ceRNA), its action in the nucleus as a transcriptional coactivator, and its function through the polycomb repressive complex 2 (PRC2)-dependent epigenetic modifications that regulate transcriptional processes. Finally, the correlation between SNHG17 and human tumors is summarized. Its potential as a novel prognostic and diagnostic biomarker for cancer is explored especially.
Early late triassic retro-foreland basin in response to flat subduction of the Paleo-Tethyan oceanic plate, SE tibet

Syn-subduction basins bear significant implications to understand tectonic evolution of any fossil subduction zone. The late Paleozoic to early Mesozoic (Paleo-Tethyan) tectonics of the eastern and southeastern Tibetan Plateau (i.e., the Sanjiang Orogenic Belt) is featured by ocean-continent subduction systems. A huge pile of volcanic-absent sedimentary succession developed in the middle segment of the Sanjiang orogenic belt, its age and tectonic nature remain unclear. Detailed geological mapping and zircon U-Pb dating results demonstrate that the early Late Triassic volcanic-absent succession comprises the nonmarine Maichuqing Formation in the lower part and the shallow marine Sanhedong Formation in the upper part. The Maichuqing Formation consists of coarse to fine-grained sandstone, siltstone and mudstone with abundant basal erosional surfaces, trough and planar cross-beddings, ripples, mudcracks, and plant fragments. The Sanhedong Formation comprises predominantly bioclastic limestones interlayered with marl, calcareous-muddy siltstone, and calcareous sandstone with abundant bivalve fossils. Syn-sedimentation deformation structures, such as slump folds and associated normal faults are common, suggesting intense tectonism during deposition. Synthesizing sedimentary data, paleocurrent and provenance results, combined with other available data, demonstrate that the volcanic-absent succession deposited within a retro-foreland basin along the rear part of the Permian-Triassic Jomda-Weixi-Yunxian arc in response to flat-subduction of the Paleo-Tethyan Ocean during the early Late Triassic time.
D-branes and boundary states in closed string theories

In this Ph.D. thesis, we study some aspects of strings and branes. We mainly focus on anomalous D-brane couplings and on non-supersymmetric branes. In Chapter 2, we illustrate three key concepts in a field theory context: duality, supersymmetry and anomaly inflow. Chapter 3 contains an introduction to string theory, emphasizing the concepts relevant to this thesis, like string scattering amplitudes and D-brane actions. In Chapter 4, we introduce the boundary state formalism and use it to check the presence of anomalous couplings in the D-brane Wess-Zumino action. In addition, we show that this action also contains non-anomalous terms. Chapter 5 gives a BPS analysis of D-branes in D-brane backgrounds, focusing on the baryon vertex in the AdS/CFT correspondence. Chapter 6 is devoted to branes in type 0 string theory. We derive the D-brane Wess-Zumino action and the massless spectra of NS-fivebranes, and combine these ingredients to comment on type 0B S-duality. In Chapter 7, we study non-BPS D-branes in type II string theory. We propose a Wess-Zumino action for these branes, check it by computing string scattering amplitudes and show that it is consistent with the interpretation of BPS D-branes as topologically non-trivial tachyon configurations on a non-BPS D-brane.
pH mediated assemblage of carbon, nitrogen, and sulfur related microbial communities in petroleum reservoirs

Microorganisms are the core drivers of biogeochemistry processes in petroleum reservoirs and have been widely used to enhance petroleum recovery. However, systematic information about the microbial communities related to the C-N-S cycle in petroleum reservoirs under different pH conditions remains poorly understood. In this study, 16S rRNA gene data from 133 petroleum samples were collected, and 756 C-N-S related genera were detected. The Chao1 richness and Shannon diversity indices for the C-N-S-related microbial communities showed significant differences among different pH conditions and at the lowest levels in acidic conditions with pH values of 4.5–6.5. In addition, pH was the most important factor influencing the C-N-S related microbial communities and contributed to 17.95% of the variation in the methanogenesis community. A total of 55 functional genera were influenced by pH, which accounted for 42.08% of the C-N-S related genera. Among them, the genera Pseudomonas and Arcobacter were the highest and were concentrated in acidic conditions with pH values of 4.5–6.5. In parallel, 56 predicted C-N-S related genes were examined, and pH affected 16 of these genes, including putative chitinase, mcrA, mtrB, cysH, narGHIVYZ, nirK, nirB, nifA, sat, aprAB, and dsrAB. Furthermore, the co-occurrence networks of the C-N-S related microbial communities distinctly varied among the different pH conditions. The acidic environment exhibited the lowest complex network with the lowest keystone taxa number, and Escherichia-Shigella was the only keystone group that existed in all three networks. In summary, this study strengthened our knowledge regarding the C-N-S related microbial communities in petroleum reservoirs under different pH conditions, which is of great significance for understanding the microbial ecology and geochemical cycle of petroleum reservoirs.