Miracle-dz/UniFAR-FTUs huggingface dataset:
Trichromacy increases fruit intake rates of wild capuchins (Cebus capucinus imitator)

Significance Color vision variation is prevalent among neotropical monkeys. Captive studies indicate that trichromacy should confer a fruit feeding advantage. This hypothesis, however, has yet to be supported by field studies. We collected behavioral and genetic data from 72 capuchins and analyzed ca. 20,000 fruit intake events across 27 plant species. Controlling for plant species and phenological condition, we find that trichromats eat reddish, conspicuous fruits more quickly than do dichromatic (red-green colorblind) groupmates. We demonstrate an advantage of trichromacy for consuming fruit among wild monkeys. Previous research has revealed dichromatic advantage for cryptic tasks; our results suggest fruit foraging plays an important role in the maintenance of primate opsin polymorphism via balancing selection. Intraspecific color vision variation is prevalent among nearly all diurnal monkeys in the neotropics and is seemingly a textbook case of balancing selection acting to maintain genetic polymorphism. Clear foraging advantages to monkeys with trichromatic vision over those with dichromatic “red-green colorblind” vision have been observed in captive studies; however, evidence of trichromatic advantage during close-range foraging has been surprisingly scarce in field studies, perhaps as a result of small sample sizes and strong impacts of environmental or individual variation on foraging performance. To robustly test the effects of color vision type on foraging efficiency in the wild, we conducted an extensive study of dichromatic and trichromatic white-faced capuchin monkeys (Cebus capucinus imitator), controlling for plant-level and monkey-level variables that may affect fruit intake rates. Over the course of 14 months, we collected behavioral data from 72 monkeys in Sector Santa Rosa, Costa Rica. We analyzed 19,043 fruit feeding events within 1,602 foraging bouts across 27 plant species. We find that plant species, color conspicuity category, and monkey age class significantly impact intake rates, while sex does not. When plant species and age are controlled for, we observe that trichromats have higher intake rates than dichromats for plant species with conspicuously colored fruits. This study provides clear evidence of trichromatic advantage in close-range fruit feeding in wild monkeys. Taken together with previous reports of dichromatic advantage for finding cryptic foods, our results illuminate an important aspect of balancing selection maintaining primate opsin polymorphism.
Synchronized chaotic targeting and acceleration of surface chemistry in prebiotic hydrothermal microenvironments

Significance We describe a physical mechanism capable of achieving simultaneous mixing and focused enrichment in hydrothermal pore microenvironments. Microscale chaotic advection established in response to a temperature gradient paradoxically promotes bulk homogenization of molecular species, while at the same time transporting species to discrete targeted locations on the bounding sidewalls where they become highly enriched. This process delivers an order of magnitude acceleration in surface reaction kinetics under conditions naturally found in subsea hydrothermal microenvironments, suggesting a new avenue to explain prebiotic emergence of macromolecules from dilute organic precursors—a key unanswered question in the origin of life on Earth and elsewhere. Porous mineral formations near subsea alkaline hydrothermal vents embed microenvironments that make them potential hot spots for prebiotic biochemistry. But, synthesis of long-chain macromolecules needed to support higher-order functions in living systems (e.g., polypeptides, proteins, and nucleic acids) cannot occur without enrichment of chemical precursors before initiating polymerization, and identifying a suitable mechanism has become a key unanswered question in the origin of life. Here, we apply simulations and in situ experiments to show how 3D chaotic thermal convection—flows that naturally permeate hydrothermal pore networks—supplies a robust mechanism for focused accumulation at discrete targeted surface sites. This interfacial enrichment is synchronized with bulk homogenization of chemical species, yielding two distinct processes that are seemingly opposed yet synergistically combine to accelerate surface reaction kinetics by several orders of magnitude. Our results suggest that chaotic thermal convection may play a previously unappreciated role in mediating surface-catalyzed synthesis in the prebiotic milieu.
Cochlear Implant Electrode Localization Using an Ultra-High Resolution Scan Mode on Conventional 64-Slice and New Generation 192-Slice Multi-Detector Computed Tomography.

HYPOTHESIS A new generation 192-slice multi-detector computed tomography (MDCT) clinical scanner provides enhanced image quality and superior electrode localization over conventional MDCT. BACKGROUND Currently, accurate and reliable cochlear implant electrode localization using conventional MDCT scanners remains elusive. METHODS Eight fresh-frozen cadaveric temporal bones were implanted with full-length cochlear implant electrodes. Specimens were subsequently scanned with conventional 64-slice and new generation 192-slice MDCT scanners utilizing ultra-high resolution modes. Additionally, all specimens were scanned with micro-CT to provide a reference criterion for electrode position. Images were reconstructed according to routine temporal bone clinical protocols. Three neuroradiologists, blinded to scanner type, reviewed images independently to assess resolution of individual electrodes, scalar localization, and severity of image artifact. RESULTS Serving as the reference standard, micro-CT identified scalar crossover in one specimen; imaging of all remaining cochleae demonstrated complete scala tympani insertions. The 192-slice MDCT scanner exhibited improved resolution of individual electrodes (p < 0.01), superior scalar localization (p < 0.01), and reduced blooming artifact (p < 0.05), compared with conventional 64-slice MDCT. There was no significant difference between platforms when comparing streak or ring artifact. CONCLUSION The new generation 192-slice MDCT scanner offers several notable advantages for cochlear implant imaging compared with conventional MDCT. This technology provides important feedback regarding electrode position and course, which may help in future optimization of surgical technique and electrode design.
Nucleic Acid Extraction from Synthetic Mars Analog Soils for in situ Life Detection

Abstract Biological informational polymers such as nucleic acids have the potential to provide unambiguous evidence of life beyond Earth. To this end, we are developing an automated in situ life-detection instrument that integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG) instrument. Our goal is to isolate and determine the sequence of nucleic acids from extant or preserved life on Mars, if, for example, there is common ancestry to life on Mars and Earth. As is true of metagenomic analysis of terrestrial environmental samples, the SETG instrument must isolate nucleic acids from crude samples and then determine the DNA sequence of the unknown nucleic acids. Our initial DNA extraction experiments resulted in low to undetectable amounts of DNA due to soil chemistry–dependent soil-DNA interactions, namely adsorption to mineral surfaces, binding to divalent/trivalent cations, destruction by iron redox cycling, and acidic conditions. Subsequently, we developed soil-specific extraction protocols that increase DNA yields through a combination of desalting, utilization of competitive binders, and promotion of anaerobic conditions. Our results suggest that a combination of desalting and utilizing competitive binders may establish a “universal” nucleic acid extraction protocol suitable for analyzing samples from diverse soils on Mars. Key Words: Life-detection instruments—Nucleic acids—Mars—Panspermia. Astrobiology 17, 747–760.
Low FODMAP: A Preliminary Strategy to Reduce Gastrointestinal Distress in Athletes

Introduction Gastrointestinal (GI) distress in endurance athletes is prevalent and detrimental to performance. Adverse GI symptomatology can be analogous with irritable bowel syndrome, where fermentable oligosaccharide, disaccharide, monosaccharide, and polyols (FODMAP) reduction has demonstrated efficacy. This study investigated the effects of low FODMAP (LFOD) diet on GI distress parameters in runners with a history of nonclinical exercise-associated GI symptoms. Methods Eleven recreationally competitive runners (five men, six women; 5-km personal best 23:00 ± 4:02 min:s) participated in the study. Runners were allocated to a randomized 6-d LFOD or high FODMAP (HFOD) diet separated by a 1-d wash-out in a controlled, single-blinded cross-over study. In each period participants completed two strenuous running sessions consisting of 5 × 1000 m and a 7-km threshold run. GI symptoms (during-exercise and daily) and the Daily Analysis of Life Demand for Athletes questionnaires were completed. Area under the curve was calculated for daily GI symptoms across each dietary period and analysis was conducted using multilevel mixed-effects linear regression for comparison between the two diets. Results A significantly smaller area under the curve for daily GI symptoms 6 d during the LFOD compared with HFOD (mean difference, −13.4; 95% confidence interval, −22 to −4.60; P = 0.003) was observed. The daily GI symptoms that were significantly lower during LFOD were flatulence (P < 0.001), urge to defecate (P = 0.04), loose stool (P = 0.03), and diarrhea (P = 0.004). No significant differences in during exercise symptoms or Daily Analysis of Life Demand for Athletes responses were observed between diets (P > 0.05). Conclusions Preliminary findings suggest that short-term FODMAP reduction may be a beneficial intervention to minimize daily GI symptoms in runners with exercise-related GI distress.
Transitivity, Space, and Hand: The Spatial Grounding of Syntax

Previous research has linked the concept of number and other ordinal series to space via a spatially oriented mental number line. In addition, it has been shown that in visual scene recognition and production, speakers of a language with a left-to-right orthography respond faster to and tend to draw images in which the agent of an action is located to the left of the patient. In this study, we aim to bridge these two lines of research by employing a novel method that measures the spatial bias produced by transitive sentences that use a wide variety of abstract and concrete verbs. Across four experiments, participants read sentences and then responded to probe words appearing on either the left or right sides of the screen. Probe words consisted of agents, patients, other words in the sentence, or newly encountered words. We found consistent lateral biases to responding to agents and patients, which appears to be independent of order of mention in the sentence but which does reflect a correspondence between position in the sentence and role in the causal sequence of the action. Our results also show that this spatial bias is driven by the use of the hands in two different ways: The left hand shows a greater sensitivity to the spatial effect than the right hand, and vocal responses produce no spatial effect.
Internal Affairs: Tenascin-C as a Clinically Relevant, Endogenous Driver of Innate Immunity

To protect against danger, the innate immune system must promptly and accurately sense alarm signals, and mount an appropriate response to restore homeostasis. One endogenous trigger of immunity is tenascin-C, a large hexameric protein of the extracellular matrix. Upregulated upon tissue injury and cellular stress, tenascin-C is expressed during inflammation and tissue remodeling, where it influences cellular behavior by interacting with a multitude of molecular targets, including other matrix components, cell surface proteins, and growth factors. Here, we discuss how these interactions confer upon tenascin-C distinct immunomodulatory capabilities that make this matrix molecule necessary for efficient tissue repair. We also highlight in vivo studies that provide insight into the consequences of misregulated tenascin-C expression on inflammation and fibrosis during a wide range of inflammatory diseases. Finally, we examine how its unique expression pattern and inflammatory actions make tenascin-C a viable target for clinical exploitation in both diagnostic and therapeutic arenas.
A review of personalized blood glucose prediction strategies for T1DM patients

This paper presents a methodological review of models for predicting blood glucose (BG) concentration, risks and BG events. The surveyed models are classified into three categories, and they are presented in summary tables containing the most relevant data regarding the experimental setup for fitting and testing each model as well as the input signals and the performance metrics. Each category exhibits trends that are presented and discussed. This document aims to be a compact guide to determine the modeling options that are currently being exploited for personalized BG prediction.
An Initial Non-Equilibrium Porous-Media Model for CFD Simulation of Stirling Regenerators

The objective of this paper is to define empirical parameters for an initial thermal non-equilibrium porous-media model for use in Computational Fluid Dynamics (CFD) codes for simulation of Stirling regenerators. The two codes currently used at Glenn Research Center for Stirling modeling are Fluent and CFD-ACE. The codes porous-media models are equilibrium models, which assume solid matrix and fluid are in thermal equilibrium. This is believed to be a poor assumption for Stirling regenerators; Stirling 1-D regenerator models, used in Stirling design, use non-equilibrium regenerator models and suggest regenerator matrix and gas average temperatures can differ by several degrees at a given axial location and time during the cycle. Experimentally based information was used to define: hydrodynamic dispersion, permeability, inertial coefficient, fluid effective thermal conductivity, and fluid-solid heat transfer coefficient. Solid effective thermal conductivity was also estimated. Determination of model parameters was based on planned use in a CFD model of Infinia's Stirling Technology Demonstration Converter (TDC), which uses a random-fiber regenerator matrix. Emphasis is on use of available data to define empirical parameters needed in a thermal non-equilibrium porous media model for Stirling regenerator simulation. Such a model has not yet been implemented by the authors or their associates.
Range of Motion Requirements for Upper-Limb Activities of Daily Living.

OBJECTIVE We quantified the range of motion (ROM) required for eight upper-extremity activities of daily living (ADLs) in healthy participants. METHOD Fifteen right-handed participants completed several bimanual and unilateral basic ADLs while joint kinematics were monitored using a motion capture system. Peak motions of the pelvis, trunk, shoulder, elbow, and wrist were quantified for each task. RESULTS To complete all activities tested, participants needed a minimum ROM of -65°/0°/105° for humeral plane angle (horizontal abduction-adduction), 0°-108° for humeral elevation, -55°/0°/79° for humeral rotation, 0°-121° for elbow flexion, -53°/0°/13° for forearm rotation, -40°/0°/38° for wrist flexion-extension, and -28°/0°/38° for wrist ulnar-radial deviation. Peak trunk ROM was 23° lean, 32° axial rotation, and 59° flexion-extension. CONCLUSION Full upper-limb kinematics were calculated for several ADLs. This methodology can be used in future studies as a basis for developing normative databases of upper-extremity motions and evaluating pathology in populations.
Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq

Poorly differentiated (PD) hepatocellular carcinoma (HCC) has a worse prognosis compared to moderately differentiated (MD) and well differentiated (WD) HCC. We aimed to identify differentially expressed genes (DEGs) to explore the mechanism of PD HCC. Transcriptome sequencing was performed on tumor and adjacent non-tumorous tissues of PD, MD and WD HCC patients (3 for each group). DEGs were thus identified and functionally analyzed. Further RT-PCR was performed to validate DEGs specific for PD HCC in 47 pairs of samples (15 for PD, 18 for MD, 14 for WD). A total of 681 PD DEGs were detected, including 368 up-regulated and 313 down-regulated genes. Less DEGs were found for MD and especially for WD HCC. Through bioinformatics analysis, PD HCC DEGs were enriched in liver tissue and liver cancer cells, and in biological process and pathway including metabolism, cell cycle, translation and blood coagulation. Potential drugs and genetic perturbations were found to reverse the cancer condition. The RT-PCR results showed consistency with RNA-seq in the validation of 4 DEGs specific for PD HCC. This study detected and validated DEGs of PD HCC, which provides useful information on molecular mechanism of PD HCC for development of new biomarkers, therapeutic targets and drugs.
Towards a Unified Complexity Theory of Total Functions

Abstract The class TFNP, of NP search problems where all instances have solutions, appears not to have complete problems. However, TFNP contains various syntactic subclasses and important problems. We introduce a syntactic class of problems that contains these known subclasses, for the purpose of understanding and classifying TFNP problems. This class is defined in terms of the search for an error in a concisely-represented formal proof. Finally, the known complexity subclasses are based on existence theorems that hold for finite structures; from Herbrand's Theorem, we note that such theorems must apply specifically to finite structures, and not infinite ones.
Early structural and functional signature of 3‐day human skeletal muscle disuse using the dry immersion model

Our study contributes to the characterization of muscle loss and weakness processes induced by a sedentary life style, chronic hypoactivity, clinical bed rest, immobilization and microgravity. This study, by bringing together integrated and cellular evaluation of muscle structure and function, identifies the early functional markers and biomarkers of muscle deconditioning. Three days of muscle disuse in healthy adult subjects is sufficient to significantly decrease muscle mass, tone and force, and to induce changes in function relating to a weakness in aerobic metabolism and muscle fibre denervation. The outcomes of this study should be considered in the development of an early muscle loss prevention programme and/or the development of pre‐conditioning programmes required before clinical bed rest, immobilization and spaceflight travel.
Impact of Type 2 Myocardial Infarction (MI) on Hospital‐Level MI Outcomes: Implications for Quality and Public Reporting

Background The International Classification of Diseases (ICD) coding system does not recognize type 2 myocardial infarction (MI) as a separate entity; therefore, patients with type 2 MI continue to be categorized under the general umbrella of non–ST‐segment–elevation myocardial infarction (NSTEMI). We aim to evaluate the impact of type 2 MI on hospital‐level NSTEMI metrics and discuss the implications for quality and public reporting. Methods and Results We conducted a single‐center retrospective analysis of 1318 patients discharged with a diagnosis of NSTEMI between July 2013 and October 2014. The Third Universal Definition was used to define type 1 and type 2 MI. Weighted Kaplan–Meier curves were used to analyze risk of mortality and readmission. Overall, 1039 patients met NSTEMI criteria per the Third Universal Definition; of those, 264 (25.4%) had type 2 MI. Patients with type 2 MI were older, were more likely to have chronic kidney disease, and had lower peak troponin levels. Compared with type 1 MI patients, those with type 2 MI had higher inpatient mortality (17.4% versus 4.7%, P<0.0001) and were more likely to die from noncardiovascular causes (71.7% versus 25.0%, P<0.0001). Despite weighting for patient characteristics and discharge medications, patients with type 2 MI had higher mortality at both 30 days (risk ratio: 3.63; 95% confidence interval, 1.67–7.88) and 1 year (risk ratio: 1.98; 95% confidence interval, 1.44–2.73) after discharge. Type 2 MI was also associated with a lower 30‐day cardiovascular‐related readmission (risk ratio: 0.49; 95% confidence interval, 0.12–2.06). Conclusions NSTEMI metrics are significantly affected by type 2 MI patients. Type 2 MI patients have distinct etiologies, are managed differently, and have higher mortality compared with patients with type 1 MI. Moving forward, it may be appropriate to exclude type 2 MI data from NSTEMI quality metrics.
The Atypical Chemokine Receptor ACKR2 is Protective Against Sepsis

ABSTRACT Sepsis is a systemic inflammatory response as a result of uncontrolled infections. Neutrophils are the first cells to reach the primary sites of infection, and chemokines play a key role in recruiting neutrophils. However, in sepsis chemokines could also contribute to neutrophil infiltration to vital organs leading to multiple organ failure. ACKR2 is an atypical chemokine receptor, which can remove and degrade inflammatory CC chemokines. The role of ACK2 in sepsis is unknown. Using a model of cecal ligation and puncture (CLP), we demonstrate here that ACKR2 deficient (−/−) mice exhibited a significant reduction in the survival rate compared with similarly treated wild-type (WT) mice. However, neutrophil migration to the peritoneal cavity and bacterial load were similar between WT and ACKR2−/− mice during CLP. In contrast, ACKR2−/− mice showed increased neutrophil infiltration and elevated CC chemokine levels in the lung, kidney, and heart compared with the WT mice. In addition, ACKR2−/− mice also showed more severe lesions in the lung and kidney than those in the WT mice. Consistent with these results, WT mice under nonsevere sepsis (90% survival) had higher expression of ACKR2 in these organs than mice under severe sepsis (no survival). Finally, the lungs from septic patients showed increased number of ACKR2+ cells compared with those of nonseptic patients. Our data indicate that ACKR2 may have a protective role during sepsis, and the absence of ACKR2 leads to exacerbated chemokine accumulation, neutrophil infiltration, and damage to vital organs.