Miracle-dz/UniFAR-FTUs huggingface dataset:
Alongshore Propagation of Subtidal Sea Level Fluctuations Around the Korean Peninsula Over Varying Stratification and Shelf Topography

Understanding subtidal (a period band of 3–20 days) coastal sea level fluctuations is of increasing importance for the sustainable use of coastal areas under challenging conditions resulting from regional and global sea-level rise. The wind-forced coastal-trapped waves (CTW) theory often accounts for subtidal sea level fluctuations observed off global coasts with a considerable range of propagation speeds. Here, the propagation speeds of subtidal sea level fluctuations observed at seven coastal tide-gauge stations around the Korean Peninsula (KP) from 1997 to 2017 were compared with phase speeds modeled for 10 segments of realistic bottom topography around the KP and four seasons of density stratification using a wind-forced CTW model. Alongshore variations in the modeled phase speed (2.0–10.0 m s–1, increasing with the bottom depth, shelf width, and vertical density difference) were consistent with those of the observed propagation speed (4.7–18.9 m s–1), despite systematic underestimation by 50%, i.e., the mean speed of 6.0 vs. 11.8 m s–1. This underestimation is discussed considering subtidal sea level fluctuations of non-CTW origin that were not incorporated into the CTW model, such as (1) Barometric sea level response to atmospheric pressure disturbances, and (2) Upwelling/downwelling response to local alongshore wind stress. This study suggests that subtidal coastal sea level fluctuates around the KP within and beyond CTW dynamics.
Bioinformatic Approach to Unveil Key Differentially Expressed Proteins in Human Sperm After Slow and Rapid Cryopreservation

Currently, two conventional freezing techniques are used in sperm cryopreservation: slow freezing (SF) and rapid freezing (RF). Despite the protocolar improvements, cryopreservation still induces significant alterations in spermatozoon that are poorly understood. Here, available proteomic data from human cryopreserved sperm was analyzed through bioinformatic tools to unveil key differentially expressed proteins (DEPs) that can be used as modulation targets or quality markers. From the included proteomic studies, 160 and 555 DEPs were collected for SF and RF groups, respectively. For each group, an integrative network was constructed using gene ontology and protein-protein interaction data to identify key DEPs. Among them, arylsulfatase A (ARSA) was highlighted in both freezing networks, and low ARSA levels have been associated with poor-sperm quality. Thus, ARSA was selected for further experimental investigation and its levels were assessed in cryopreserved samples by western blot. ARSA levels were significantly decreased in RF and SF samples (∼31.97 and ∼39.28%, respectively). The bioinformatic analysis also revealed that the DEPs were strongly associated with proteasomal and translation pathways. The purposed bioinformatic approach allowed the identification of potential key DEPs in freeze-thawed human spermatozoa. ARSA has the potential to be used as a marker to assess sperm quality after cryopreservation.
Structural Insights Into Tautomeric Dynamics in Nucleic Acids and in Antiviral Nucleoside Analogs

DNA (2′-deoxyribonucleic acid) and RNA (ribonucleic acid) play diverse functional roles in biology and disease. Despite being comprised primarily of only four cognate nucleobases, nucleic acids can adopt complex three-dimensional structures, and RNA in particular, can catalyze biochemical reactions to regulate a wide variety of biological processes. Such chemical versatility is due in part to the phenomenon of nucleobase tautomerism, whereby the bases can adopt multiple, yet distinct isomeric forms, known as tautomers. For nucleobases, tautomers refer to structural isomers that differ from one another by the position of protons. By altering the position of protons on nucleobases, many of which play critical roles for hydrogen bonding and base pairing interactions, tautomerism has profound effects on the biochemical processes involving nucleic acids. For example, the transient formation of minor tautomers during replication could generate spontaneous mutations. These mutations could arise from the stabilization of mismatches, in the active site of polymerases, in conformations involving minor tautomers that are indistinguishable from canonical base pairs. In this review, we discuss the evidence for tautomerism in DNA, and its consequences to the fidelity of DNA replication. Also reviewed are RNA systems, such as the riboswitches and self-cleaving ribozymes, in which tautomerism plays a functional role in ligand recognition and catalysis, respectively. We also discuss tautomeric nucleoside analogs that are efficacious as antiviral drug candidates such as molnupiravir for coronaviruses and KP1212 for HIV. The antiviral efficacy of these analogs is due, in part, to their ability to exist in multiple tautomeric forms and induce mutations in the replicating viral genomes. From a technical standpoint, minor tautomers of nucleobases are challenging to identify directly because they are rare and interconvert on a fast, millisecond to nanosecond, time scale. Nevertheless, many approaches including biochemical, structural, computational and spectroscopic methods have been developed to study tautomeric dynamics in RNA and DNA systems, and in antiviral nucleoside analogs. An overview of these methods and their applications is included here.
Temporary Shutdown of ERK1/2 Phosphorylation Is Associated With Activation of Adaptive Immune Cell Responses and Disease Progression During Leishmania amazonensis Infection in BALB/c Mice

Leishmania spp. infection outcomes are dependent on both host and parasite factors. Manipulation of host signaling pathways involved in the generation of immune responses is thought to be one of the most common mechanisms used by parasites for persistence within the host. Considering the diversity of pathologies caused by different Leishmania spp. , it is plausible that significant differences may exist in the mechanisms of host cell manipulation by each parasite species, which may have implications when developing new vaccine or treatment strategies. Here we show that in L. braziliensis-infection in BALB/c mice, a model of resistance, activation of ERK1/2 coincides with the peak of inflammatory responses and resolution of tissue parasitism. In contrast, in the susceptibility model of L. amazonensis-infection, an early silent phase of infection is observed, detected solely by quantification of parasite loads. At this early stage, only basal levels of P-ERK1/2 are observed. Later, after a brief shutdown of ERK1/2 phosphorylation, disease progression is observed and is associated with increased inflammation, lesion size and tissue parasitism. Moreover, the short-term down-regulation of ERK1/2 activation affected significantly downstream inflammatory pathways and adaptive T cell responses. Administration of U0126, a MEK/ERK inhibitor, confirmed this phenomenon, since bigger lesions and higher parasite loads were seen in infected mice that received U0126. To investigate how kinetics of ERK1/2 activation could affect the disease progression, U0126 was administered to L. amazonensis-infected animals earlier than the P-ERK1/2 switch off time-point. This intervention resulted in anticipation of the same effects on inflammatory responses and susceptibility phenotype seen in the natural course of infection. Additionally, in vitro inhibition of ERK1/2 affected the phagocytosis of L. amazonensis by BMDMs. Collectively, our findings reveal distinct temporal patterns of activation of inflammatory responses in L. braziliensis and L. amazonensis in the same animal background and a pivotal role for a brief and specific shutdown of ERK1/2 activation at late stages of L. amazonensis infection. Since activation of inflammatory responses is a crucial aspect for the control of infectious processes, these findings may be important for the search of new and specific strategies of vaccines and treatment for tegumentary leishmaniasis.
Mangosteen Peel Liquid-Protected Soybean Meal Can Shift Rumen Microbiome and Rumen Fermentation End-Products in Lactating Crossbred Holstein Friesian Cows

Rumen bypass protein can enhance protein availability in the lower gut. This study investigated the use of liquid-containing phytonutrients in dairy cows as a dietary additives to reduce rumen protein degradation. Four crossbred lactating Holstein Friesian cows (75% Holstein Friesian with 25% Thai native breed) with an initial body weight (BW) of 410 ± 20 kg were randomly assigned to a 2 × 2 factorial arrangement [two crude protein (CP) levels with soybean meal (SBM) or mangosteen peel liquid-protected soybean meal (MPLP)-SBM] in a 4 × 4 Latin square design experiment. Dietary treatments were as follows: T1 = SBM in low crude protein concentrate (LPC) (SBM-LPC); T2 = MPLP-SBM in LPC (MPLP-SBM-LPC); T3 = SBM in high crude protein concentrate (HPC) (SBM-HPC); T4 = MPLP-SBM in HPC (MPLP-SBM-HPC). Apparent digestibilities of organic matter (OM) and neutral detergent fiber (aNDF) were increased (p < 0.05) by CP level in the HPC diet (19% CP), with higher OM and aNDF digestibilities. High crude protein concentrate increased (p < 0.05) the propionic acid in the rumen but reduced (p < 0.05) the acetic acid-to-propionic acid ratio and methane (CH4) production. Rumen microbial populations of the total bacteria, Fibrobacter succinogenes and Butyrivibrio fibrisolvens were increased (p < 0.05) by HPC. Real-time PCR revealed a 30.6% reduction of rumen methanogens by the MPLP-SBM in HPC. Furthermore, efficiency of microbial nitrogen synthesis (EMNS) was 15.8% increased (p < 0.05) by the MPLP-SBM in HPC when compared to SBM-LPC. Milk yield and milk composition protein content were enhanced (p < 0.05) by both the CP level in concentrate and by MPLP inclusion. In this experiment, a high level of CP and the MPLP-SBM enhanced the ruminal propionate, shifted rumen microbiome, and enhanced milk yield and compositions.
Origin and Demographic History of Philippine Pigs Inferred from Mitochondrial DNA

The Philippines is a mega-diverse country that lies at the crossroads of past human migrations in the Asia-Pacific region and is believed to have never been connected to the Asian continent, even during the major sea-level subsidence of the Quaternary. As a result, the history of pig dispersal in the Philippines remains controversial, due to limited molecular studies and absence of archaeological evidence of pig domestication. This study provides the first comprehensive analysis of 184 complete mitochondrial DNA D-loop region from Philippine pigs to elucidate their early dispersal history by performing a phylogenetic comparison with wild boars and domestic pigs worldwide. The results showed a demographic signal of the ancestry of Philippine pigs that had a close genetic relationship with those from the mainland Southeast Asia and Northeast Asia, suggesting gene flow that may have resulted from human migration and trade. Here we have suggested two possible dispersal routes. One parallels the Neolithic expansion in Island Southeast Asia and Oceania via Northeast Asia, the other from the mainland Southeast Asia, into Palawan and Sulu Archipelago as early as prehistoric times via the Sundaic Region. Despite geographic barriers to migration, numerous genetic lineages have persisted across the Philippine islands, even justifying the recognition of a Philippine Lanyu subclade. The prehistoric population history suggests a demographic expansion that coincided with the interglacial periods of the Pleistocene and may have spread from the southern regions into the eastern and central regions of the Philippines. The intriguing signal of discrepancy discovered between the ancestral pattern and distribution range of the numerous endemic Philippine wild pigs opens a challenging new approach to illuminate complexity among these animals. Our study has contributed significantly towards completing the sparse molecular studies on Philippine pigs, an essential for creating win-win conservation measures.
The Influence of Stress on Decision-Making: Effects of CRF and Dopamine Antagonism in the Nucleus Accumbens

The actions of corticotropin-releasing factor (CRF) in the core of the nucleus accumbens including increasing dopamine release and inducing conditioned place preference in stress-naïve animals. However, following two-day, repeated forced swim stress (rFSS), neither of these effects are present, indicating a stress-sensitive interaction between CRF and dopamine. To ascertain the degree to which this mechanism influences integrated, reward-based decision making, we used an operant concurrent-choice task where mice could choose between two liquid receptacles containing a sucrose solution or water delivery. Following initial training, either a CRF or dopamine antagonist, α-helical CRF (9–41) and flupenthixol, respectively, or vehicle was administered intracranially to the nucleus accumbens core. Next, the animals underwent rFSS, were reintroduced to the task, and were retested. Prior to stress, mice exhibited a significant preference for sucrose over water and made more total nose pokes into the sucrose receptacle than the water receptacle throughout the session. There were no observed sex differences. Stress did not robustly affect preference metrics but did increase the number of trial omissions compared to their stress-naïve, time-matched counterparts. Interestingly, flupenthixol administration did not affect sucrose choice but increased their nosepoke preference during the inter-trial interval, increased trial omissions, and decreased the total nosepokes during the ITI. In contrast, microinjections of α-helical CRF (9–41) did not affect omissions or ITI nosepokes but produced interactions with stress on choice metrics. These data indicate that dopamine and CRF both interact with stress to impact performance in the task but influence different behavioral aspects.
Contrasting Impacts of Climate Warming on Coastal Old-Growth Tree Species Reveal an Early Warning of Forest Decline

Old-growth forests in the Pacific Northwest are being fundamentally altered by climate change. A primary example of this is yellow-cedar (Callitropsis nootkatensis), a culturally and economically important species, which has suffered widespread decline across its range since the beginning of the twentieth century. We used tree rings to compare the climate-growth response of yellow-cedar to two co-occurring species; western hemlock (Tsuga heterophylla) and Sitka spruce (Picea sitchensis), in an old-growth forest on Haida Gwaii, Canada, to better understand the unique climatic drivers of a species that is declining across its range. We developed three species-specific chronologies spanning 560–770 years, reconstructing a long-term record of species growth and dynamics over time. The climate is strongly influenced by the Pacific Decadal Oscillation (PDO), a multi-decadal pattern of ocean-atmospheric climate variability. Climate varied across three time periods that have coincided with major shifts in the PDO during the twentieth century [1901–1945 (neutral/positive), 1946–1976 (negative) and 1977–2015 (positive)]. Conditions were significantly warmer and wetter during positive phases, with the greatest maximum temperatures in the most recent period. We used complimentary methods of comparison, including Morlet wavelet analysis, Pearson correlations, and linear-mixed effects modeling to investigate the relations between climate and species growth. All three species exhibited multi-decadal frequency variation, strongest for yellow-cedar, suggesting the influence of the PDO. Consistent with this, the strength and direction of climate-growth correlations varied among PDO phases. Growing season temperature in the year of ring formation was strongly positively correlated to yellow-cedar and western hemlock growth, most significantly in the latter two time periods, representing a release from a temperature limitation. Sitka spruce growth was only weakly associated with climate. Yellow-cedar responded negatively to winter temperature from 1977 to 2015, consistent with the decline mechanism. Increased yellow-cedar mortality has been linked to warmer winters and snow loss. This study provides new insights into yellow-cedar decline, finding the first evidence of decline-related growth patterns in an apparently healthy, productive coastal temperate rainforest.
Intratumor Microbiome Analysis Identifies Positive Association Between Megasphaera and Survival of Chinese Patients With Pancreatic Ductal Adenocarcinomas

Human tumors harbor a plethora of microbiota. It has been shown that the composition and diversity of intratumor microbiome are significantly associated with the survival of patients with pancreatic ductal adenocarcinoma (PDAC). However, the association in Chinese patients as well as the effect of different microorganisms on inhibiting tumor growth are unclear. In this study, we collected tumor samples resected from long-term and short-term PDAC survivors and performed 16S rRNA amplicon sequencing. We found that the microbiome in samples with different survival time were significantly different, and the differential bacterial composition was associated with the metabolic pathways in the tumor microenvironment. Furthermore, administration of Megasphaera, one of the differential bacteria, induced a better tumor growth inhibition effect when combined with the immune checkpoint inhibitor anti-programmed cell death-1 (anti-PD-1) treatment in mice bearing 4T1 tumor. These results indicate that specific intratumor microbiome can enhance the anti-tumor effect in the host, laying a foundation for further clarifying the underlying detailed mechanism.
Structure design of Mach-Zehnder interferometer in electrooptic integrated acceleration seismic geophone

A novel electrooptic integrated acceleration seismic geophone was presented.Mach-Zehnder waveguide interferometer of Si-based MOEMS(micro-optoelectro-mechanical system)acceleration seismic geophone was researched and its optimization structure design was accomplished.The material of buffer layer and coating layer is K9 glass.Two Bak7 glass Y-branching waveguides with width of 4 μm and thickness of 0.4 μm,and six guide mirrors are employed in interferometer. A S-shaped curve is used for the transition connecting two offset parallel waveguides in Y-branching.Because it is difficulty to make the branching angle large enough by using conventional Y-branching,a 90° directional change by a vertical mirror facet to realize the special structure between measuring arm and reference arm is designed.The inner dielectric film of the mirror facet is aluminum plating.To prevent the polarization state of TE mode polarized light from changing after passing through the aluminum film,4 polarizers with length of 1 mm have been used.The simulation results performed in BPM and the experiment agrees with the theoretical analysis well.
Axonal and Dendritic Morphology of Excitatory Neurons in Layer 2/3 Mouse Barrel Cortex Imaged Through Whole-Brain Two-Photon Tomography and Registered to a Digital Brain Atlas

Communication between cortical areas contributes importantly to sensory perception and cognition. On the millisecond time scale, information is signaled from one brain area to another by action potentials propagating across long-range axonal arborizations. Here, we develop and test methodology for imaging and annotating the brain-wide axonal arborizations of individual excitatory layer 2/3 neurons in mouse barrel cortex through single-cell electroporation and two-photon serial section tomography followed by registration to a digital brain atlas. Each neuron had an extensive local axon within the barrel cortex. In addition, individual neurons innervated subsets of secondary somatosensory cortex; primary somatosensory cortex for upper limb, trunk, and lower limb; primary and secondary motor cortex; visual and auditory cortical regions; dorsolateral striatum; and various fiber bundles. In the future, it will be important to assess if the diversity of axonal projections across individual layer 2/3 mouse barrel cortex neurons is accompanied by functional differences in their activity patterns.
Surgical Process Modeling for Open Spinal Surgeries

Modern operating rooms are becoming increasingly advanced thanks to the emerging medical technologies and cutting-edge surgical techniques. Current surgeries are transitioning into complex processes that involve information and actions from multiple resources. When designing context-aware medical technologies for a given intervention, it is of utmost importance to have a deep understanding of the underlying surgical process. This is essential to develop technologies that can correctly address the clinical needs and can adapt to the existing workflow. Surgical Process Modeling (SPM) is a relatively recent discipline that focuses on achieving a profound understanding of the surgical workflow and providing a model that explains the elements of a given surgery as well as their sequence and hierarchy, both in quantitative and qualitative manner. To date, a significant body of work has been dedicated to the development of comprehensive SPMs for minimally invasive baroscopic and endoscopic surgeries, while such models are missing for open spinal surgeries. In this paper, we provide SPMs common open spinal interventions in orthopedics. Direct video observations of surgeries conducted in our institution were used to derive temporal and transitional information about the surgical activities. This information was later used to develop detailed SPMs that modeled different primary surgical steps and highlighted the frequency of transitions between the surgical activities made within each step. Given the recent emersion of advanced techniques that are tailored to open spinal surgeries (e.g., artificial intelligence methods for intraoperative guidance and navigation), we believe that the SPMs provided in this study can serve as the basis for further advancement of next-generation algorithms dedicated to open spinal interventions that require a profound understanding of the surgical workflow (e.g., automatic surgical activity recognition and surgical skill evaluation). Furthermore, the models provided in this study can potentially benefit the clinical community through standardization of the surgery, which is essential for surgical training.