Miracle-dz/UniFAR-FTUs huggingface dataset:
Migrating bison engineer the green wave

Significance The Green Wave Hypothesis (GWH) says the green wave—the progression of spring green-up from low to high elevations or latitudes—dictates the pace of herbivore migrations worldwide. Animals move in sync with the wave because young vegetation provides the best forage. We show the GWH needs to be revised to include group-forming grazers that not only move to find forage, but create forage by how they move. Bison, by moving and grazing en masse, release themselves from the need to “surf the wave. ” Their movements and grazing stimulate plant growth and delay plant maturation, which allows them to eat high-quality foods despite falling behind the wave while also modifying the progression of the green wave itself. Newly emerging plants provide the best forage for herbivores. To exploit this fleeting resource, migrating herbivores align their movements to surf the wave of spring green-up. With new technology to track migrating animals, the Green Wave Hypothesis has steadily gained empirical support across a diversity of migratory taxa. This hypothesis assumes the green wave is controlled by variation in climate, weather, and topography, and its progression dictates the timing, pace, and extent of migrations. However, aggregate grazers that are also capable of engineering grassland ecosystems make some of the world’s most impressive migrations, and it is unclear how the green wave determines their movements. Here we show that Yellowstone’s bison (Bison bison) do not choreograph their migratory movements to the wave of spring green-up. Instead, bison modify the green wave as they migrate and graze. While most bison surfed during early spring, they eventually slowed and let the green wave pass them by. However, small-scale experiments indicated that feedback from grazing sustained forage quality. Most importantly, a 6-fold decadal shift in bison density revealed that intense grazing caused grasslands to green up faster, more intensely, and for a longer duration. Our finding broadens our understanding of the ways in which animal movements underpin the foraging benefit of migration. The widely accepted Green Wave Hypothesis needs to be revised to include large aggregate grazers that not only move to find forage, but also engineer plant phenology through grazing, thereby shaping their own migratory movements.
ITPK1 mediates the lipid-independent synthesis of inositol phosphates controlled by metabolism

Significance Inositol phosphates (IPs) are a class of signaling molecules regulating cell physiology. The best-characterized IP, the calcium release factor IP3, is generated by phospholipase C hydrolysis of phosphoinositides lipids. For historical and technical reasons, IPs synthesis is believed to originate from the lipid-generated IP3. While this is true in yeast, our work has demonstrated that other organisms use a “soluble” (nonlipid) route to synthesize IPs. This soluble pathway depends on the metabolic status of the cells, and is under the control of the kinase ITPK1, which phosphorylates inositol monophosphate likely generated from glucose. The data shed light on the evolutionary origin of IPs, signaling and tightening the link between these small molecules and basic metabolism. Inositol phosphates (IPs) comprise a network of phosphorylated molecules that play multiple signaling roles in eukaryotes. IPs synthesis is believed to originate with IP3 generated from PIP2 by phospholipase C (PLC). Here, we report that in mammalian cells PLC-generated IPs are rapidly recycled to inositol, and uncover the enzymology behind an alternative “soluble” route to synthesis of IPs. Inositol tetrakisphosphate 1-kinase 1 (ITPK1)—found in Asgard archaea, social amoeba, plants, and animals—phosphorylates I(3)P1 originating from glucose-6-phosphate, and I(1)P1 generated from sphingolipids, to enable synthesis of IP6. We also found using PAGE mass assay that metabolic blockage by phosphate starvation surprisingly increased IP6 levels in a ITPK1-dependent manner, establishing a route to IP6 controlled by cellular metabolic status, that is not detectable by traditional [3H]-inositol labeling. The presence of ITPK1 in archaeal clades thought to define eukaryogenesis indicates that IPs had functional roles before the appearance of the eukaryote.
One-Step Hydrothermal Synthesis of P25 @ Few Layered MoS2 Nanosheets toward Enhanced Bi-catalytic Activities: Photocatalysis and Electrocatalysis

P25 loaded few layered molybdenum disulfide (MoS2) nanosheets (P25@MoS2) are successfully synthesized through a facile one-step hydrothermal process. The bi-catalytic activities, i.e., photocatalytic and electrocatalytic activities, of the as-prepared nanomaterials have been investigated. For the as-prepared products, the photocatalytic performances were investigated by degrading simulated pollutant under sunlight irradiation, and the hydrogen evolution reaction evaluated the electrocatalytic performances. The results indicate that P25@MoS2 possesses excellent activities in both photocatalysis and electrocatalysis. The presence of MoS2 broadens the light absorption range of P25 and improves the separation and transformation efficiency of photogenerated carriers, thus improving its photocatalytic performance. The existence of P25 inhibits the aggregation of MoS2 to form more dispersed MoS2 nanosheets with only few layers increasing its active sites. Thereby, the electrocatalytic performance is heightened. The excellent multifunction makes the as-prepared P25@MoS2 a promising material in the fields of environment and energy.
A Novel Benthic Phage Infecting Shewanella with Strong Replication Ability

The coastal sediments were considered to contain diverse phages playing important roles in driving biogeochemical cycles based on genetic analysis. However, till now, benthic phages in coastal sediments were very rarely isolated, which largely limits our understanding of their biological characteristics. Here, we describe a novel lytic phage (named Shewanella phage S0112) isolated from the coastal sediments of the Yellow Sea infecting a sediment bacterium of the genus Shewanella. The phage has a very high replication capability, with the burst size of ca. 1170 phage particles per infected cell, which is 5–10 times higher than that of most phages isolated before. Meanwhile, the latent period of this phage is relatively longer, which might ensure adequate time for phage replication. The phage has a double-stranded DNA genome comprising 62,286 bp with 102 ORFs, ca. 60% of which are functionally unknown. The expression products of 16 ORF genes, mainly structural proteins, were identified by LC-MS/MS analysis. Besides the general DNA metabolism and structure assembly genes in the phage genome, there is a cluster of auxiliary metabolic genes that may be involved in 7-cyano-7-deazaguanine (preQ0) biosynthesis. Meanwhile, a pyrophosphohydrolase (MazG) gene being considered as a regulator of programmed cell death or involving in host stringer responses is inserted in this gene cluster. Comparative genomic and phylogenetic analysis both revealed a great novelty of phage S0112. This study represents the first report of a benthic phage infecting Shewanella, which also sheds light on the phage–host interactions in coastal sediments.
Streamlined particle quantification (SParQ) plug-in is an automated fluorescent vesicle quantification plug-in for particle quantification in Fiji/ImageJ

ABSTRACT The endolysosomal system is critical for protein homeostasis in cells. A common way of studying protein transport and degradation (e.g. via autophagy) is by labeling vesicular structures such as endosomes, autophagosomes, lysosomes, or model substrates with fluorescent tags or by fluorescent antibody staining. Detailed analyses require quantification of hundreds of structures under various conditions. Typically, the images are analyzed individually with software such as the widely available Fiji/ImageJ (https://imagej.net/Fiji/Downloads), adjusting and thresholding each image and channel independently, which is a very labor intensive and fastidious task. To streamline the process, we developed a plug-in that, integrated into Fiji, enables the automated quantification of vesicular (i.e. punctate) structures. Importantly, the process still allows the operator to evaluate and have control over all the phases of quantification process. Abbreviations CMA: chaperone-mediated autophagy; CSV: comma separated values; eMI: endosomal microautophagy; Fiji: Fiji is just ImageJ; MA: macroautophagy; SParQ: Streamlined Particle Quantification
Optical Coherence Tomography Angiography in Amblyopia.

BACKGROUND AND OBJECTIVE The posterior segment of the eye has been investigated in the pathogenesis of amblyopia, but no abnormalities have yet been reported consistently. PATIENTS AND METHODS In this prospective study, treatment-naïve amblyopes aged 6 years to 12 years with best-corrected visual acuity in the amblyopic eye between logMAR 0.3 and logMAR 0.7 and logMAR 0.1 or better in the contralateral eye were recruited. All patients underwent optical coherence tomography angiography (OCTA) imaging of the retina and choriocapillaris. RESULTS The mean age of the 14 recruited patients was 10.26 years ± 1.31 years. The choriocapillaris vessel density was found to be attenuated in the amblyopic eye as compared to the fellow eye. There was a significant difference in the choriocapillaris vessel density between the amblyopic (39.61% ± 0.45%), and the fellow eye (44.10% ± 0.37%; P = .005). The choriocapillaris vessel density correlated positively with the visual acuity (r = 0.41; P = .03). CONCLUSION The pathogenesis of amblyopia may involve the choriocapillaris, which is the primary source of blood supply for the photoreceptors. [Ophthalmic Surg Lasers Imaging Retina. 2019;50:e294-e299. ].
Differentiation of leukemic blasts is not completely blocked in acute myeloid leukemia

Significance A long-held tenet in acute myeloid leukemia (AML) is that multiple genetic events produce a block in the differentiation of primitive myeloblast cells. Using mathematical modeling, we show that, rather than a complete block, even a slight reduction or skewing of the differentiation rate in these cells produces an AML phenotype. We experimentally validated that mature myeloid cells have the same genotype as leukemic blasts, demonstrating that there is not a complete block in differentiation. While targeted differentiation therapies have shown success in isolated subtypes of AML, our findings suggest that maximizing the potential impact of these agents will require discernment of the specific actionable mechanisms underlying reduced or skewed differentiation in genetic subtypes of the disease. Hematopoiesis, the formation of blood cells, involves the hierarchical differentiation of immature blast cells into mature, functional cell types and lineages of the immune system. Hematopoietic stem cells precisely regulate self-renewal versus differentiation to balance the production of blood cells and maintenance of the stem cell pool. The canonical view of acute myeloid leukemia (AML) is that it results from a combination of molecular events in a hematopoietic stem cell that block differentiation and drive proliferation. These events result in the accumulation of primitive hematopoietic blast cells in the blood and bone marrow. We used mathematical modeling to determine the impact of varying differentiation rates on myeloblastic accumulation. Our model shows that, instead of the commonly held belief that AML results from a complete block of differentiation of the hematopoietic stem cell, even a slight skewing of the fraction of cells that differentiate would produce an accumulation of blasts. We confirmed this model by interphase fluorescent in situ hybridization (FISH) and sequencing of purified cell populations from patients with AML, which showed that different leukemia-causing molecular abnormalities typically thought to block differentiation were consistently present in mature myeloid cells such as neutrophils and monocytes at similar levels to those in immature myeloid cells. These findings suggest reduced or skewed, rather than blocked, differentiation is responsible for the development of AML. Approaches that restore normal regulation of hematopoiesis could be effective treatment strategies.
Emerging serine-threonine kinase inhibitors for treating ovarian cancer

ABSTRACT Introduction: Ovarian cancer is the leading cause of gynecologic cancer death, owing to high rates of incurable, recurrent disease after initial treatment. Serine threonine kinases (STKs) have been proposed as potential therapeutic targets in ovarian cancer because of their role in the initiation and progression of cancers. Experience in non-ovarian cancers suggests that STK inhibitors are active against tumors with specific molecular alterations. Areas covered: This review discusses STK inhibitors in active development in phase II/III clinical trials for ovarian cancer. PubMed and ClinicalTrials.gov were systematically searched to identify STK inhibitor trials for ovarian cancer; active development was confirmed via Pharmaprojects. Available data regarding the efficacy and safety of these compounds are explored. Expert opinion: STK inhibitors currently in development have modest activity as single agents and are unlikely to achieve approval as monotherapy for unselected ovarian cancer patients. Combination trials of STK inhibitors with chemotherapy and/or targeted therapies have suggested an acceptable efficacy/toxicity ratio for certain combinations but confirmatory studies are needed. Carefully designed trials, especially those including somatic molecular analysis, may help identify the subsets of patients most likely to benefit from these therapeutic strategies and determine the role of STK inhibitors in the evolving landscape of precision oncology.
Methods to collect and interpret external training load using microtechnology incorporating GPS in professional football: a systematic review

ABSTRACT The aim of this article was to systematically review the methods adopted to collect and interpret external training load (ETL) using microtechnology incorporating global positioning system (GPS). The main deficiencies identified concerned the non-collection of match ETL, and the non-consideration of potential confounders (e.g. playing position, fitness level, starting status or session content). Also, complementary training (individual/reconditioning) and pre-match warm-up were rarely quantified. To provide a full picture of the training demands, ETL was commonly complemented by internal training load monitoring with the rating of perceived exertion predominantly adopted instead of heart rate recordings. Continuous data collection and interpretation of ETL data in professional football vary widely between observational studies, possibly reflecting the actual procedures adopted in practical settings. Evidence about continuous ETL monitoring in female players, and female as well as male goalkeepers is lacking.
Anaesthetists’ drug dosing practices in class III obese surgical patients: A bi-national survey

Class III obese (body mass index ≥ 40 kg/m2) patients, now regularly encountered clinically, have increased perioperative risks, including potentially from suboptimal drug dosing. However, current dosing guidelines are based on low-level evidence and may not be widely accepted. This study aimed to investigate anaesthetists’ dosing practices for class III obese surgical patients, explore if they had experienced an increased incidence of adverse events potentially related to drug dosing with these patients and assess which resources they consulted for dosing advice in this population. An electronic survey was emailed to 1000 randomly selected members of the Australian and New Zealand College of Anaesthetists. Data were summarised and the Pearson’s χ2 test was used to compare respondents’ genders, geographic locations and seniority designations with the greater Australian and New Zealand College of Anaesthetists’ membership. There were 230 completed responses (response rate 23%). A large proportion (46%–76%) of respondents indicated they dose class III obese patients in keeping with current recommendations; however, substantial heterogeneity in dosing practices was found. Lean body weight was the most frequently used regimen for dosing propofol, non-depolarising muscle relaxants, sugammadex and opioids, whereas total body weight was most frequently used for suxamethonium. Nearly 70% of respondents reported using at least one resource to assist their dosing practices in obesity. Importantly, increased incidences of adverse events in class III obese patients related to drug dosing were commonly experienced by respondents. Until higher-level evidence is available for dosing class III obese patients, anaesthetists should consider current recommendations and exercise increased attention to dosing. Further clinician education may assist in optimising dosing in this patient group.
Cardiovascular risk with androgen deprivation therapy

From the primary care perspective, many urologists and oncologists appear to be ignoring an FDA warning to assess patients' cardiovascular (CV) risk before instituting androgen deprivation therapy (ADT) with gonadotropin‐releasing hormone (GnRH) agonists. A growing body of data suggest an association between ADT and CV/cardiometabolic risk, particularly for GnRH agonists.
Multivariate Analysis of Joint Motion Data by Kinect: Application to Parkinson’s Disease

Analysis of joint motion data (AJMD) by Kinect, such as velocity, has been widely used in many research fields, many of which focused on how one joint moves with another, namely bivariate AJMD. However, these studies might not accurately reflect the motor symptoms in patients. The human body can be divided into six widely accepted parts (head, trunk and four limbs), which are interrelated and interact with each other. Therefore, in this study we attempted to investigate how the major joints of one body part move with the ones in another body part, namely multivariate AJMD. For method illustration, the motion data of sit-to-stand-to-sit for healthy participants and people with Parkinson disease (PD) were employed. Four types of multivariate AJMD were investigated by eigenspace-maximal-information-canonical-correlation-analysis, which obtained maximal- information-eigen-coefficients (MIECes), the parameters for quantifying the correlation between two sets of joints located in two different body parts. The results show that healthy participants have significantly higher MIECes than the PD patients (p-value < 0.0001). Furthermore, the area under the receiver operating characteristic curve value for the classification between healthy participants and PD patients reaches up to 1.00. In conclusion, we demonstrated the possibility of using multivariate AJMD for motion feature extraction, which may be helpful for medical research and engineering.
Plocabulin Displays Strong Cytotoxic Activity in a Personalized Colon Cancer Patient-Derived 3D Organoid Assay

Plocabulin is a novel microtubule-disrupting antitumor agent of marine origin that is currently undergoing phase II clinical trials. Plocabulin has potent antiproliferative and antiangiogenic actions in carcinoma cell lines and has antitumor activity in xenografted mice. Here, we used three-dimensional (3D) tumor organoids derived from three colorectal cancer (CRC) patients to study the effect of plocabulin in a personalized assay system that ensures dose dependence and high reproducibility. The cytotoxicity of plocabulin was an order of magnitude higher than that of the active irinotecan derivative SN38 (7-ethyl-10-hydroxy-camptothecin) in tumor organoids at different passages. Moreover, plocabulin maintained its strong cytotoxic activity in wash-out experiments, in which a short pulse treatment of tumor organoids was as efficient as continuous treatment. Our data show that plocabulin has a very potent cytotoxic action in CRC patient-derived tumor organoids, supporting ongoing clinical trials with plocabulin and the use of organoid assays to provide personalized validation of antitumor drugs.
TFregulomeR reveals transcription factors’ context-specific features and functions

Abstract Transcription factors (TFs) are sequence-specific DNA binding proteins, fine-tuning spatiotemporal gene expression. Since genomic occupancy of a TF is highly dynamic, it is crucial to study TF binding sites (TFBSs) in a cell-specific context. To date, thousands of ChIP-seq datasets have portrayed the genomic binding landscapes of numerous TFs in different cell types. Although these datasets can be browsed via several platforms, tools that can operate on that data flow are still lacking. Here, we introduce TFregulomeR (https://github.com/benoukraflab/TFregulomeR), an R-library linked to an up-to-date compendium of cistrome and methylome datasets, implemented with functionalities that facilitate integrative analyses. In particular, TFregulomeR enables the characterization of TF binding partners and cell-specific TFBSs, along with the study of TF’s functions in the context of different partnerships and DNA methylation levels. We demonstrated that TFs’ target gene ontologies can differ notably depending on their partners and, by re-analyzing well characterized TFs, we brought to light that numerous leucine zipper TFBSs derived from ChIP-seq experiments documented in current databases were inadequately characterized, due to the fact that their position weight matrices were assembled using a mixture of homodimer and heterodimer binding sites. Altogether, analyses of context-specific transcription regulation with TFregulomeR foster our understanding of regulatory network-dependent TF functions.
Early Identification of Dropout-Prone Students and Early Intervention Strategies to Improve Student Retention at a Private University

The problem of this study was first year student retention at a private university. The purpose of the study was to identify high risk students (dropout prone) by use of the Stratil Counseling Inventory -_ College Form (SCI-C) in order to initiate early intervention counseling and advising. Intrusive counseling was started within the first six weeks of the 1984 fall semester to facilitate the students' transition to college. The population of the study was first-time full-time freshmen students in attendance at Freshmen Orientation the week prior to the beginning of the 1984 academic year. SCI-C instrument consisted of six scales designed to elicit attrition-related information about the firsttime, freshmen students. The scales identified students who were in need of assistance, and they provided a profile of their problem areas. This information, available within ten days after the beginning of classes enabled Student Development personnel to select the students out of the freshman class who needed help and to refer them to university resources for assistance. The conclusions drawn from the analysis of the SCI-C data were: (1) students who needed assistance to integrate into the academic and social envrionment of the university were identified by the SCI-C; (2) students at Hardin-Simmons University value adult/student relationship outside of the classroom; (3) attitudes of caring service creates a "staying environment;1* (4) although the SCI-C indicates students' interests in support services, not all students who request assistance, avail themselves of the opportunities provided for them; (5) a relationship seems to exist between the intervention strategies provided particular freshmen and their succesful performance in the classroom (CPA of 1.60 or greater) and their persistence at the university for their second year; (6) the SCI-C provides attrition-related counseling information about students rather than predicting college academic success; and (7) the SCI-C i s a valid instrument to use to facilitate student retention at Hardin-Simmons University,