Miracle-dz/UniFAR-FTUs huggingface dataset:
Circulating immune cell phenotype dynamics reflect the strength of tumor–immune cell interactions in patients during immunotherapy

Significance The evolution of peripheral immune cell abundance and signaling over time, as well as how these immune cells interact with the tumor, may impact a cancer patient’s response to therapy. By developing an ecological population model, we provide evidence of a dynamic predator–prey-like relationship between circulating immune cell abundance and tumor size in patients that respond to immunotherapy. This relationship is not found either in patients that are nonresponsive to immunotherapy or during chemotherapy. Single-cell RNA sequencing of serial peripheral blood samples from patients shows that the strength of tumor–immune cell interactions is reflected in T cells’ interferon activation and differentiation early in treatment. Thus, circulating immune cell dynamics reflect a tumor’s response to immunotherapy. The extent to which immune cell phenotypes in the peripheral blood reflect within-tumor immune activity prior to and early in cancer therapy is unclear. To address this question, we studied the population dynamics of tumor and immune cells, and immune phenotypic changes, using clinical tumor and immune cell measurements and single-cell genomic analyses. These samples were serially obtained from a cohort of advanced gastrointestinal cancer patients enrolled in a trial with chemotherapy and immunotherapy. Using an ecological population model, fitted to clinical tumor burden and immune cell abundance data from each patient, we find evidence of a strong tumor-circulating immune cell interaction in responder patients but not in those patients that progress on treatment. Upon initiation of therapy, immune cell abundance increased rapidly in responsive patients, and once the peak level is reached tumor burden decreases, similar to models of predator–prey interactions; these dynamic patterns were absent in nonresponder patients. To interrogate phenotype dynamics of circulating immune cells, we performed single-cell RNA sequencing at serial time points during treatment. These data show that peripheral immune cell phenotypes were linked to the increased strength of patients’ tumor–immune cell interaction, including increased cytotoxic differentiation and strong activation of interferon signaling in peripheral T cells in responder patients. Joint modeling of clinical and genomic data highlights the interactions between tumor and immune cell populations and reveals how variation in patient responsiveness can be explained by differences in peripheral immune cell signaling and differentiation soon after the initiation of immunotherapy.
Recent advances of ambient ionization mass spectrometry imaging in clinical research.

The structural information and spatial distribution of molecules in biological tissues are closely related to the potential molecular mechanisms of disease origin, transfer, and classification. Ambient ionization mass spectrometry imaging is an effective tool that provides molecular images while describing in situ information of biomolecules in complex samples, in which ionization occurs at atmospheric pressure with the samples being analyzed in the native state. Ambient ionization mass spectrometry imaging can directly analyze tissue samples at a fairly high resolution to obtain molecules in situ information on the tissue surface to identify pathological features associated with a disease, resulting in the wide applications in pharmacy, food science, botanical research and especially clinical research. Herein, novel ambient ionization techniques, such as techniques base on spray and solid-liquid extraction, techniques base on plasma desorption, techniques base on laser desorption ablation and techniques base on acoustic desorption were introduced, and the data processing of ambient ionization mass spectrometry imaging was briefly reviewed. Besides, we also highlight recent applications of this imaging technology in clinical researches and discuss the challenges in this imaging technology and the perspectives on the future of the clinical research. This article is protected by copyright. All rights reserved.
Pectinaria chilensis NILSSON, 1928 (POLYCHAETA: PECTINARIIDAE): taxonomic characterization, new distributional records and ecological notes from the chilean coast

SUMMARY The taxonomy, geographical distribution, and ecological aspects of Pectinaria chilensis are reviewed. Specimens were collected in sublittoral soft bottoms, between 45 and 93m depth, at four localities in northern Chile. These specimens are compared with individuals collected from 17m depth at Coronel, Gulf of Arauco, Chile, the type locality of the species. A taxonomic characterization, illustrations and a list of new localities in the geographical distribution of this species are presented. Ecological information (bathymetry, sediment type, total organic matter content and dissolved O 2 concentration of sea water above the bottom) is included, as well as a key for differentiating the two Pectinariidae species registered in Chile to date. RESUMEN Se revisa Pectinaria chilensis de la costa de Chile a partir de ejemplares recolectados en fondos blandos sublitorales, entre 45 y 93m de profundidad, en cuatro localidades del norte de Chile. Estos especimenes fueron comparados con ejemplares recolectados a 17m de profundidad en Coronel, Golfo de Arauco, Chile, localidad tipo de la especie. Se incluye una
Diagnosis & management of alpha-gal syndrome: lessons from 2,500 patients

ABSTRACT Introduction Alpha-gal Syndrome (AGS) is a unique allergy to non-primate mammalian meat (and derived-products) that is associated with tick bites and is due to a specific IgE antibody to the oligosaccharide galactose-α-1,3-galactose (alpha-gal). AGS has many novel features that broaden the paradigm of food allergy, including that reactions are delayed 3–6 hours after exposure and patients have frequently tolerated red meat for many years prior to the development of allergic reactions. Due to the ubiquitous inclusion of mammal-derived materials in foods, medications, personal products and stabilizing compounds, full avoidance is difficult to achieve. Areas covered This review describes the author’s experience with diagnosis, management, and design of appropriate avoidance for patients with AGS and provides clinicians with practical advice for care of these patients. Expert opinion The number of patients with AGS is rising and may have exceeded awareness of the diagnosis amongst healthcare providers. In summarizing experience gained to thus far, we hope to create a resource for identifying and managing this unique allergic syndrome.
Machine Learning Assisted Citation Screening for Systematic Reviews

Evidence-based practice is highly dependent upon up-to-date systematic reviews (SR) for decision making. However, conducting and updating systematic reviews, especially the citation screening for identification of relevant studies, requires much human work and is therefore expensive. Automating citation screening using machine learning (ML) based approaches can reduce cost and labor. Machine learning has been applied to automate citation screening but not for the SRs with very narrow research questions. This paper reports the results and observations for an ongoing research that aims to automate citation screening for SRs with narrow research questions using machine learning. The research also sheds light on the problem of class imbalance and class overlap on the performance of ML classifiers when applied to SRs with narrow research questions.
Multiple Stressors and Amphibians: Contributions of Adverse Health Effects and Altered Hydroperiod to Population Decline and Extinction

Abstract Amphibian decline is a well-recognized globally occurring problem. Hypothesized and demonstrated causes of decline are varied and include disease, contaminants, habitat loss, and climate change. Future research and management efforts may be further improved by understanding how different anthropogenic stress factors contribute to amphibian population declines for different species. I used a stochastic, density-dependent population model of the pool-breeding amphibian, Gastrophryne carolinensis, to explore the relative contribution of different simulated stress factors operating individually and in combination on a number of different life-cycle components. The simulations revealed that catastrophic reproductive failure (CRF) as may occur under climate-induced reductions in hydroperiod was a strong driver of extinction risk and that, in the absence of CRF, extinction risks were low (<1%) even under some reduction in recruitment and terrestrial survival for this species. When reductions in vital rates and CRF occurred together, extinction risks increased pointing to the importance of multiple factors as potential drivers of amphibian decline. The results presented here suggest that climate change-induced alterations in hydroperiod may have severe consequences for declines of some amphibian populations. Further, the presence of additional stress factors only serves to increase risk. In addition to the need for studies of stressor effects on components of amphibian life cycles, future research and conservation efforts should consider the interaction of stressors acting on the health of individuals (disease, pollution) and temporal variation in environmental factors such as hydroperiod.
Secretome Analysis of Mesenchymal Stem Cell Factors Fostering Oligodendroglial Differentiation of Neural Stem Cells In Vivo

Mesenchymal stem cell (MSC)-secreted factors have been shown to significantly promote oligodendrogenesis from cultured primary adult neural stem cells (aNSCs) and oligodendroglial precursor cells (OPCs). Revealing underlying mechanisms of how aNSCs can be fostered to differentiate into a specific cell lineage could provide important insights for the establishment of novel neuroregenerative treatment approaches aiming at myelin repair. However, the nature of MSC-derived differentiation and maturation factors acting on the oligodendroglial lineage has not been identified thus far. In addition to missing information on active ingredients, the degree to which MSC-dependent lineage instruction is functional in vivo also remains to be established. We here demonstrate that MSC-derived factors can indeed stimulate oligodendrogenesis and myelin sheath generation of aNSCs transplanted into different rodent central nervous system (CNS) regions, and furthermore, we provide insights into the underlying mechanism on the basis of a comparative mass spectrometry secretome analysis. We identified a number of secreted proteins known to act on oligodendroglia lineage differentiation. Among them, the tissue inhibitor of metalloproteinase type 1 (TIMP-1) was revealed to be an active component of the MSC-conditioned medium, thus validating our chosen secretome approach.
Identifying hotspots of cardiometabolic outcomes based on a Bayesian approach: The example of Chile

Background There is a need to identify priority zones for cardiometabolic prevention. Disease mapping in countries with high heterogeneity in the geographic distribution of the population is challenging. Our goal was to map the cardiometabolic health and identify hotspots of disease using data from a national health survey. Methods Using Chile as a case study, we applied a Bayesian hierarchical modelling. We performed a cross-sectional analysis of the 2009–2010 Chilean Health Survey. Outcomes were diabetes (all types), obesity, hypertension, and high LDL cholesterol. To estimate prevalence, we used individual and aggregated data by province. We identified hotspots defined as prevalence in provinces significantly greater than the national prevalence. Models were adjusted for age, sex, their interaction, and sampling weight. We imputed missing data. We applied a joint outcome modelling approach to capture the association between the four outcomes. Results We analysed data from 4,780 participants (mean age (SD) 46 (19) years; 60% women). The national prevalence (percentage (95% credible intervals) for diabetes, obesity, hypertension and high LDL cholesterol were 10.9 (4.5, 19.2), 30.0 (17.7, 45.3), 36.4 (16.4, 57.6), and 13.7 (3.4, 32.2) respectively. Prevalence of diabetes was lower in the far south. Prevalence of obesity and hypertension increased from north to far south. Prevalence of high LDL cholesterol was higher in the north and south. A hotspot for diabetes was located in the centre. Hotspots for obesity were mainly situated in the south and far south, for hypertension in the centre, south and far south and for high LDL cholesterol in the far south. Conclusions The distribution of cardiometabolic risk factors in Chile has a characteristic pattern with a general trend to a north-south gradient. Our approach is reproducible and demonstrates that the Bayesian approach enables the accurate identification of hotspots and mapping of disease, allowing the identification of areas for cardiometabolic prevention.
CHARACTERIZATION OF HYPOTHALAMIC NEUROPEPTIDES IN MAMMALIAN REPRODUCTION

Understanding of regulation of reproduction at the level of the brain changed dramatically with the discovery of reproductive neuropeptides. To date there have been no studies to characterize the distribution of reproductive neuropeptides in the bovine hypothalamus at different stages of the estrus cycle or to determine the physiological effects of peripheral administration of Gonadotropin inhibiting hormone (GnIH) in intact female cattle and ovariohysterectomized bitches. The goal of the first study was to determine distribution and connectivity of kisspeptin, dynorphin, and GnIH in the hypothalami of sexually mature female cattle during the estrous cycle. To this end, hypothalami of female cattle were collected during periestrus and diestrus. The neuroanatomical distribution, synaptic connectivity, and response to different circulating progesterone concentrations suggest these neuropeptides play a pivotal role in the regulation of reproduction in cyclic cattle. Another goal was to test the hypothesis that IV administration of GnIH would decrease serum LH concentrations in post-pubertal heifers. Two studies were carried out to this end. The objective of the first study was to determine whether IV GnIH administration would decrease basal serum LH concentrations. The objective of the second study was to determine whether continuous IV administration of GnIH during the expected time of the LH surge had an effect on serum LH concentrations and ovulation. Results suggest that exogenous administration of GnIH decreases basal LH concentrations but is not able to suppress the surge release of LH or ovulation in post-pubertal heifers. Finally, the objective of the third study was to determine the effects of IV administration of GnIH on serum LH concentrations in ovariohysterectomized bitches as a potential alternative to surgical sterilization. Results suggest that IV administration of GnIH is not able to suppress serum LH concentrations in the ovariohysterectomized bitch.
Health Professionals' Experiences of the Benefits and Challenges of Online Symptom Checkers

Online symptom checkers and assessment services are used by patients seeking guidance on health problems. In this study, the goal was to identify health professionals' experiences of the benefits and challenges of new symptom checkers providing triage advice. Data was collected through an online survey of 61 health professionals who were target users of the online symptom checkers implemented in six public health organizations and one private occupational health clinic. Most of the health professionals supported the use of online symptom checkers and found services useful to patients because they provided patients quick contact with health professionals and referral to care or self-management instructions regardless of time and place. Health professionals were less confident that most of the patients were capable and willing to use the symptom checkers. Health professionals were satisfied with symptom checkers providing them with more useful information before meeting patients. By contrast, symptom checkers were seen as disrupting clinical work and time-consuming. The results imply that the clinical work processes should be redesigned to guide patients in an efficient manner, avoid work overlap, and provide work motivation for professionals.
Postpartum Group Cohesion of Sympatric Deer in Texas

Abstract Postpartum behavior of maternal deer may be specific to species of deer and predators. We captured sympatric white-tailed deer (Odocoileus virginianus) and mule deer (O. hemionus eremicus) fawns from radiocollared adult females in 2004–2006 on rangelands of west central Texas, USA, where predators larger than bobcats (Lynx rufus) were absent. Our objective was to determine whether differences in postpartum antipredator behavior existed between deer species, and if so, examine efficacy of those strategies. We collected postpartum group cohesion data in 2004 and 2005 by using radiotelemetry and examined dead fawns for cause of mortality. During fawns' hider phase, <3 weeks postpartum, mule deer females kept fawns closer to themselves (95% CI = 39–66 m) and twins closer to each other (95% CI = 25–49 m) than did white-tailed deer females (95% CIs = 152–234 m and 163–255 m, respectively). After 30 days postpartum, familial group cohesion was similarly tight for both species. During hider phases from 2004 to 2006, predated carcasses of white-tailed deer fawns (11 of 11) were dismembered or consumed more than mule deer fawns (7 of 13, P = 0.016), which was one line of evidence for maternal defense by mule deer adults. During hider phases in 2004 and 2005, predation rate of mule deer fawns was lower than that for white-tailed deer fawns. In 2006, predation rate increased for mule deer but was similar for white-tailed deer fawns compared with previous years. The tight cohesion strategy of mule deer exhibited in 2004 and 2005 seemed successful at thwarting small predators. Without large predators, the loose cohesion strategy of white-tailed deer females was maladaptive. When meso-predators are abundant due to extermination of larger predators, predation on fawns could increase if a deer species has relatively fixed postpartum maternal antipredator behavior.
Mechanism for diffe rential desiccation tolerance in porphyra species

Drought has been the cause of most agricultural losses, and therefore it is not surprising that desiccation has been one of the most studied stresses on plants. As a result, the mechanisms that desiccation tolerant terrestrial plants use to survive drought conditions are well understood today. This is not the case for those macrophytic marine algae (or seaweeds) that grow in the intertidal zone on rocky shores, which experience far more rapid and severe losses of water content than terrestrial plants. The goal of this study was to determine the mechanism of desiccation tolerance in seaweeds using the Red algae Porphyra umbilicalis and P. yezoensis as a model system. While these two algae have very different tolerances to desiccation, this study showed that both species lost about 95% of their water in the first two hours of dehydration and their final relative water content is virtually the same. Massive membrane leakage, reduced respiration and reduced oxygen evolution were observed in P. yezoensis after desiccation, but not in P. umbilicalis. TEM observation revealed extensive membrane disruption only in P. yezoensis after desiccation. Reactive oxygen species (ROS) defense, repression of membrane phase transition and formation of cellular glass are the three major desiccation tolerance mechanisms reported in land plants. ROS defense is not the key to the difference between P. umbilicalis and P. yezoensis for several reasons. First, desiccation in the dark did not alleviate the desiccation damage in P. yezoensis, as light has been shown to stimulate ROS damage. P. yezoensis also had higher superoxide dismutase activity. There was a small decrease in ascorbate content in P. umblicalis after desiccation, but such decrease
Description of a new species of Bush Warbler of the genus Cettia Bonaparte, 1834 (Aves: Sylviidae) from Yamdena, Tanimbar Islands, Indonesia

The use of mistnets in forest on Yamdena (Tanimbar Islands, South Moluccas, Indonesia) revealed the presence of an undescribed bush-warbler of the genus Cettia Bonaparte, 1834. The new species is described and illustrated here and its morphological characters and vocalizations are compared with those of Asian-Pacific congeners in the subgenus Horeites Hodgson, 1845. It is considered most closely related to the Southwest Pacific warblers previously known as Vitia Ramsay, 1875. In addition, the identity of Cettia bivittata Finsch, 1901, is discussed.
Isolation and characterization of DNA microsatellite primers for Cynoscion acoupa, the most exploited sciaenid fish along the coast of Brazil

The northern mangrove coast of Brazil comprises the Brazilian states of Amapa, Para and Maranhao. Fishes from the coastal mangrove region form a principal component of the local fishery, and account for 58% of all fish landed. The most commonly landed fishes are those of the family Sciaenidae. Cynoscion acoupa is one of the most exploited sciaenid species, with over 600 tons landed each year. Therefore, we developed 17 microsatellite markers to investigate genetic variability and population structuring of this species along the coast of Brazil.
Reproductive biology of Hilsa shad (Tenualosa ilisha) in coastal waters of the Northwest of Persian Gulf.

Some aspects of the reproductive biology of Hilsa Shad, Tenualosa ilisha from the Persian Gulf and rivers of Khouzestan Province of Iran were analyzed. A total of 485 fish were sampled by gillnet from landing center of Arvand (AR) and Bahmanshir (BR) rivers during period of April 2010 to September 2010. Reproductive characteristic of T.ilisha showed that sex ratio is M: F=1:2, in PG, AR and BR. This means that females predominate than males. Monthly variations in Gonadosomatic index (GSI) of both sexes were quite apparent. In PG, maximum values were recorded in April for male and female. In AR and BR, maximum values were recorded in June and May for male and female, respectively. Changes in GSI indices are considered as a proof that maturation season in AR and BR is started from March and spawning is started from April to July in AR and BR is started from March to August. The Length - Weight relationship was measured for PG as W= 1.459L 2.687 , AR and BR as W=2.189L 3.166 and W=1.840L 2.937 , respectively.
Bioenergetics Modeling in the 21st Century : Reviewing New Insights and Revisiting Old Constraints

Abstract The development and application of fish bioenergetics models have flourished in recent years, due in part to the complexity of the issues being faced by fisheries biologists. As with any model, the accuracy of bioenergetics models can be hampered by uncertainty in model parameters. A review of the literature showed that field and laboratory tests of bioenergetics models often result in poor agreement between model predictions and independent data. Nonetheless, bioenergetics modeling continues to be used to make important management decisions. Recent tests of model predictions have shown that parameter uncertainty is influenced by factors such as feeding rate, physiological adaptations, and prey composition and abundance. In an attempt to reduce the uncertainty in modeling applications, we propose a framework that highlights the importance of (1) model evaluation, (2) hypothesis-based parameter testing, and (3) improved communication between model developers and model users. Adherence to this fram.