Miracle-dz/UniFAR-FTUs huggingface dataset:
Sex Differences in Renal Ammonia Metabolism.

Sexual dimorphic variations are present in many aspects of biology and involve the structure and/or function of nearly every organ system. Acid-base homeostasis is critical for optimal health, and renal ammonia metabolism has a major role in the maintenance of acid-base homeostasis. Recent studies have shown sex-dependent differences in renal ammonia metabolism with regards to both basal ammonia excretion and the response to an exogenous acid load. These sexual dimorphisms are associated with structural changes in the proximal tubule and the collecting duct and variations in the expression of multiple proteins involved in ammonia metabolism and transport. Studies using orchiectomy (ORCH)-induced testosterone deficiency and physiological testosterone replacement show testosterone underlies much of the sex-dependent differences in the proximal tubule. This parallels the finding that the canonical testosterone target receptor, androgen receptor (AR), is present exclusively in the proximal tubule. Thus, testosterone, possibly acting through AR activation, regulates multiple coponents of renal structure and ammonia metabolism. The lack of detectable AR in the remainder of the nephron and the collecting duct suggests that some dimorphisms in renal structure and ammonia transporter expression are mediated through mechanisms other than direct testosterone-dependent AR activation. A better understanding of the mechanism and biological implications of sex's effect on renal structure and ammonia metabolism is critical for optimizing our ability to care for both men and women with acid-base disturbances.
Electron-transfer pathways in the primary event of bacterial photosynthesis

The photochemical reaction in bacterial photosynthesis is the transfer of an electron from a bacteriochlorophyll dimer (P) to a bacteriopheophytin (H), possibly by way of another bacteriochlorophyll (B). The authors explore the mechanism of this reaction by calculating quantum-mechanical matrix elements for the electronic coupling of the exciton states and intermolecular charge-transfer (CT) states of the photosynthetic reaction center. The calculations are based on the crystal structure of the Rhodopseudomonas viridis reaction center and on semiempirical atomic resonance integrals. Five possible mechanisms for charge separation are considered. The matrix elements for a pathway via the intermediate CT state P/sup +/B/sup -/ are consistent with the experimentally measured kinetics of the reaction, but this pathway requires a remarkable stabilization of the CT state by the protein. An alternative pathway via B/sup +/H/sup -/ could be more favorable energetically, but has somewhat smaller coupling elements.
Multiparametric High‐Content Assays to Measure Cell Health and Oxidative Damage as a Model for Drug‐Induced Liver Injury

Drug‐induced liver injury is an important cause of non‐approval in drug development and the withdrawal of already approved drugs from the market. Screening human hepatic cell lines for toxicity has been used extensively to predict drug‐induced liver injury in preclinical drug development. Assessing hepatic‐cell health with more diverse markers will increase the value of in vitro assays and help predict the mechanism of toxicity. We describe three live cell‐based assays using HepG2 cells to measure cell health parameters indicative of hepatotoxicity. The first assay measures cellular ATP levels using luciferase. The second and third assays are multiparametric high‐content screens covering a panel of cell health markers including cell count, mitochondrial membrane potential and structure, nuclear morphology, vacuolar density, and reactive oxygen species and glutathione levels. © 2020 Wiley Periodicals LLC.
Thiophene and Selenophene Copolymers Incorporating Fluorinated Phenylene Units in the Main Chain: Synthesis, Characterization, and Application in Organic Field-Effect Transistors

A series of thiophene oligomers bearing core phenylene and fluorinated phenylene units has been synthesized as potential semiconductor materials for organic field-effect transistors (OFETs). Polymerization of these compounds has been achieved using Stille and oxidative Coupling methods. Functionalization of the phenylene unit with fluorine atoms has a marked effect on the self-assembly and electronic properties of the parent materials: the optical band gaps and highest occupied molecular orbital levels are affected with the introduction Of fluorine atoms as a result of a combination of inductive effects and rigidification of the main chain. The design of these materials has focused on the self-assembly and solution processability of the materials. All the polymers are readily Soluble in common organic solvents. Self-assembly and planarization of the fluorinated materials in the solid state are identified by a combination of X-ray diffraction studies, absorption spectroscopy, and cyclic voltammetry. The organizational behavior of the films is in contrast to the conformational freedom observed in solution (absorption spectroscopy) and in the gas phase (computational Studies). Thin-film OFETs have been fabricated for the entire polymer series. Hole mobilities have been measured Lip to 10(-3) cm(2)/(V(.)s), with high current modulation (on/off ratios up to 10(5)) and low turn-on voltages (down to 2 V). For the Stille Coupled polymers, replacement of the bridging thiophene unit with selenophene generally increases the hole mobility of the polymers.
Adaptive Rehabilitation Bots in Serious Games †

In recent years, we have witnessed a growing adoption of serious games in telerehabilitation by taking advantage of advanced multimedia technologies such as motion capture and virtual reality devices. Current serious game solutions for telerehabilitation suffer form lack of personalization and adaptiveness to patients’ needs and performance. This paper introduces “RehaBot”, a framework for adaptive generation of personalized serious games in the context of remote rehabilitation, using 3D motion tracking and virtual reality environments. A personalized and versatile gaming platform with embedded virtual assistants, called “Rehab bots”, is created. Utilizing these rehab bots, all workout session scenes will include a guide with various sets of motions to direct patients towards performing the prescribed exercises correctly. Furthermore, the rehab bots employ a robust technique to adjust the workout difficulty level in real-time to match the patients’ performance. This technique correlates and matches the patterns of the precalculated motions with patients’ motions to produce a highly engaging gamified workout experience. Moreover, multimodal insights are passed to the users pointing out the joints that did not perform as anticipated along with suggestions to improve the current performance. A clinical study was conducted on patients dealing with chronic neck pain to prove the usability and effectiveness of our adjunctive online physiotherapy solution. Ten participants used the serious gaming platform, while four participants performed the traditional procedure with an active program for neck pain relief, for two weeks (10 min, 10 sessions/2 weeks). Feasibility and user experience measures were collected, and the results of experiments show that patients found our game-based adaptive solution engaging and effective, and most of them could achieve high accuracy in performing the personalized prescribed therapies.
The Value of Artificial Intelligence in Laboratory Medicine

Abstract Objectives As laboratory medicine continues to undergo digitalization and automation, clinical laboratorians will likely be confronted with the challenges associated with artificial intelligence (AI). Understanding what AI is good for, how to evaluate it, what are its limitations, and how it can be implemented are not well understood. With a survey, we aimed to evaluate the thoughts of stakeholders in laboratory medicine on the value of AI in the diagnostics space and identify anticipated challenges and solutions to introducing AI. Methods We conducted a web-based survey on the use of AI with participants from Roche’s Strategic Advisory Network that included key stakeholders in laboratory medicine. Results In total, 128 of 302 stakeholders responded to the survey. Most of the participants were medical practitioners (26%) or laboratory managers (22%). AI is currently used in the organizations of 15.6%, while 66.4% felt they might use it in the future. Most had an unsure attitude on what they would need to adopt AI in the diagnostics space. High investment costs, lack of proven clinical benefits, number of decision makers, and privacy concerns were identified as barriers to adoption. Education in the value of AI, streamlined implementation and integration into existing workflows, and research to prove clinical utility were identified as solutions needed to mainstream AI in laboratory medicine. Conclusions This survey demonstrates that specific knowledge of AI in the medical community is poor and that AI education is much needed. One strategy could be to implement new AI tools alongside existing tools.
CHANGES IN TOTAL INORGANIC PROFILE NITROGEN IN LONG-TERM RYE–WHEAT–RYEGRASS FORAGE PRODUCTION SYSTEM*

ABSTRACT Inorganic soil profile nitrogen (N) levels can increase with application rates greater than those necessary for maximum cereal grain yields. Forage systems are different than grain production systems in that harvest is generally prior to anthesis and gaseous plant N loss is not allowed to occur. This promotes removal of more total N from the system and results in higher nitrogen use efficiencies (NUE). Nitrogen rates representing increased profile N accumulation as well as those below this threshold were evaluated from a long-term rye–wheat–ryegrass production experiment. Nitrogen rates from 1979–1993 were 0, 56, 84, 112, 168, and 224 kg N ha−1.Rates were doubled in 1994 in an effort to add N at a rate above which no increase in forage production would be expected.Wheat was eliminated from the winter seeding mix in 1994, as it was an extremely small portion of the total harvested forage. Deep soil cores (0–366 cm) were taken during the early summer of 1996 from plots with a history of continuous fertilization and forage production since 1979.Cores were split into 15 cm (0–60 cm) or 30 cm increments (60–366 cm) and analyzed for NO3–N, NH4–N, and pH.Total inorganic N accumulations were calculated by adding NO3–N and NH4–N.Surface accumulations of NH4–N were significant with annual N rates of 224 kg N ha−1 or more. No differences in NH4–N were noted at lower depths, thus movement through the profile was not observed. Nitrate–N at the highest N rate was significantly higher than check levels down to 270 cm increasing the risk of groundwater contamination.It should be noted that the maximum N rate was increased to 448 kg ha−1 in 1994 in an attempt to determine a level above which no yield response would be noted. No increase in forage production has been consistently noted with rates over 224 kg N ha−1 and at this level the only adverse effect is increased NO3–N in the surface 90 cm. These long-term experimental results support the conclusion that nitrogen fertilizer additions at recommended rates do not increase the risk of NO3–N leaching.
Low Frequency Dispersion in Ionic Crystals

A new region of anomalous electrical response has been observed at low frequencies in ionic crystals that have been treated to introduce relatively large number of lattice defects. The crystals thus far studied include various alkali halides and silver chloride. The effect is attributed to a jumping of the positive ions to vacant lattice sites under the influence of the applied field. This jumping is observed as a relaxation process, producing a change in the dielectric constant which is small and frequently within the limits of error of measurement, and an associated peak in the dielectric loss tangent which is readily measurable. This maximum of tan δ has been studied both as a function of frequency at a fixed temperature and as a function of temperature at fixed frequency. From the magnitude of the peak and position on the frequency or temperature scales it is possible to calculate the number of lattice defects present in the sample and the activation energy for diffusion U of the positive ion in the c.
Recovery from minimally invasive vs. open surgery in kidney cancer patients: Opioid use and workplace absenteeism

Purpose Does surgical approach (minimally invasive vs. open) and type (radical vs. partial nephrectomy) affects opioid use and workplace absenteeism. Materials and Methods Retrospective multivariable regression analysis of 2,646 opioid-naïve patients between 18 and 64 undergoing radical or partial nephrectomy via either a minimally invasive vs. open approach for kidney cancer in the United States between 2012 and 2017 drawn from the IBM Watson Health Database was performed. Outcomes included: (1) opioid use in opioid-naïve patients as measured by opioid prescriptions in the post-operative setting at early, intermediate and prolonged time periods and (2) workplace absenteeism after surgery. Results Patients undergoing minimally invasive surgery had a lower odds of opioid use in the early and intermediate post-operative periods (early: odds ratio [OR], 0.77; 95% confidence interval [CI], 0.62–0.97; p=0.02, intermediate: OR, 0.60; 95% CI, 0.48–0.75; p<0.01), but not in the prolonged setting (prolonged: OR, 1.00; 95% CI, 0.75–1.34; p=0.98) and had earlier return to work (minimally invasive vs. open: −10.53 days; 95% CI, −17.79 to −3.26; p<0.01). Controlling for approach, patient undergoing partial nephrectomy had lower rates of opioid use across all time periods examined and returned to work earlier than patients undergoing radical nephrectomy (partial vs. radical: −14.41 days; 95% CI, −21.22 to −7.60; p<0.01). Conclusions Patients undergoing various forms of surgery for kidney cancer had lower rates of peri-operative opioid use, fewer days of workplace absenteeism, but no difference in long-term rates of opioid use in patients undergoing minimally invasive as compared to open surgery.
Use of 3-nitrooxypropanol in a commercial feedlot to decrease enteric methane emissions from cattle fed a corn-based finishing diet.

The study evaluated enteric CH4 production, dry matter (DM) intake (DMI), and rumen fermentation in feedlot cattle supplemented with increasing concentrations of 3-nitrooxypropanol (3-NOP). A total of 100 crossbred steers (body weight, 421 ± 11 kg) was randomly assigned to one of 4 treatments (n = 25/treatment): control (no 3-NOP), or low (100 mg/kg DM), medium (125 mg/kg DM), and high (150 mg/kg DM) doses of 3-NOP. The study was comprised of 28 days of adaptation followed by three 28-d periods, with CH4 measured for 7-d per period and cattle remaining on their respective diets throughout the 112-d study. Each treatment group was assigned to a pen, with the cattle and diets rotated among pens weekly to allow the animals to access the GreenFeed emission monitoring (GEM) system stationed in one of the pens for CH4 measurement. Measured concentration (mg/kg DM) of 3-NOP in the total diet consumed (basal diet + GEM pellet) was 85.6 for low, 107.6 for medium, and 124.5 for high doses of 3-NOP. There was a treatment × period interaction (P < 0.001) for DMI; compared to control, the DMI was less for the low and high doses in periods 1, with no differences thereafter. Compared to control (10.78 g/kg DMI), CH4 yield (g/kg DMI) was decreased (P < 0.001) by 52%, 76%, and 63% for low, medium, and high doses of 3-NOP, respectively. A treatment × period effect (P = 0.048) for CH4 yield indicated that the low dose decreased in efficacy from 59% decrease in periods 1 and 2, to 37% decrease in period 3, while efficacy of the medium and high doses remained consistent over time. Irrespective of dose, hydrogen emissions increased by 4.9-fold (P < 0.001) and acetate:propionate ratio in rumen fluid decreased (P = 0.045) with 3-NOP supplementation, confirming that other hydrogen-utilizing pathways become more important in the CH4-inhibited rumen. The study indicates that supplementation of corn-based finishing diets with 3-NOP using a medium dose is an effective CH4 mitigation strategy for commercial beef feedlots with 76% decrease in CH4 yield. Further research is needed to determine the effects of 3-NOP dose on weight gain, feed conversion efficiency, and carcass characteristics of feedlot cattle at a commercial scale.
Unzipping DNA Oligomers

We applied AFM-based single-molecule force spectroscopy to investigate the “unziping” of double-stranded DNA molecules with different sequences. The forces needed to open the double strands showed variations between 10 and 20 pN on a length scale of 10 bases. The force profiles were characteristic for each DNA sequence and could be described quantitatively using a thermodynamic equilibrium model.
Efficient photoactivatable Dre recombinase for cell type-specific spatiotemporal control of genome engineering in the mouse

Significance Precisely defining specific cell types is critical but challenging for biological studies. Site-specific tyrosine-recombinase Cre and its inducible variants have been widely used in efficient genetic engineering. However, a single recombinase system has technical hurdles. Here, a photoactivatable Dre (PA-Dre) recombinase is developed by tethering split Dre fragments to the light-inducible Magnets system. PA-Dre is efficient and stringently controlled in vitro and in vivo. Moreover, with the creation of the Cre-activated light-inducible Dre system, it is able to achieve bulk or sparse labeling of specific neurons in a spatiotemporal manner. This flexible and tunable system could be adapted to a wide range of biological systems for the modulation of developmental and genetic complexity. Precise genetic engineering in specific cell types within an intact organism is intriguing yet challenging, especially in a spatiotemporal manner without the interference caused by chemical inducers. Here we engineered a photoactivatable Dre recombinase based on the identification of an optimal split site and demonstrated that it efficiently regulated transgene expression in mouse tissues spatiotemporally upon blue light illumination. Moreover, through a double-floxed inverted open reading frame strategy, we developed a Cre-activated light-inducible Dre (CALID) system. Taking advantage of well-defined cell-type–specific promoters or a well-established Cre transgenic mouse strain, we demonstrated that the CALID system was able to activate endogenous reporter expression for either bulk or sparse labeling of CaMKIIα-positive excitatory neurons and parvalbumin interneurons in the brain. This flexible and tunable system could be a powerful tool for the dissection and modulation of developmental and genetic complexity in a wide range of biological systems.
Availability of Donor Human Milk Decreases the Incidence of Necrotizing Enterocolitis in VLBW Infants

Background: Human milk feeding is associated with decreased risk of necrotizing enterocolitis (NEC). Purpose: To determine whether a quality improvement project in New Jersey neonatal intensive care units (NICUs) to promote human milk (HM) feedings would be associated with a decrease in NEC. Methods: Fourteen New Jersey NICUs engaged in efforts to reduce infection and promote HM feeding in very low birth-weight (VLBW) infants. Donor human milk (DHM) availability and NEC rates were assessed. Results: From 2009 to 2016, NICUs with DHM increased from 0 to 7. VLBW infants discharged on any HM increased from 35% in 2007 before the formation of the New Jersey NICU Collaborative to more than 55% in 2016. Time to first oropharyngeal colostrum decreased from 37 to 30 hours from 2014 to 2016. HM at first feeding increased from 71% in 2013 to 82% in 2016. There was an increase in the percentage of feeds that were HM over the first 7 days of feeding. Analyses of data from 9400 VLBW infants born between 2009 and 2016 showed that the incidence of NEC when DHM was not available was 5.1% (367/7182) whereas the incidence when DHM was available (64/2218) was significantly lower (2.9%; P < .0001). Implications for Practice: These findings show advantages of feeding HM and effectiveness of forming an NICU collaborative for improving care for preterm infants. Implications for Research: New research projects should measure the quantity of HM consumed daily during the entire NICU stay and assess the timing and amount of HM consumption in relationship to incidence of NEC and infection in neonates.
Empirical Correlations Between Conformational Parameters in β‐D‐Furanoside Fragments Derived from a Statistical Survey of Crystal Structures of Nucleic Acid Constituents Full Description of Nucleoside Molecular Geometries in Terms of Four Parameters

A data file was created containing internal coordinates and derived parameters for 178 β-D-furanoside fragments, occurring in X-ray structures of ribo-, 2′-deoxyribo- and arabinonucleoside derivatives. The variability in bond angles and torsion angles can be described by four conformational parameters; the kind and degree of ring puckering as expressed in phase angle of pseudorotation P and puckering amplitude vm, the conformation of the side-chain δ and the glycosidic torsion angle χ. Comparison between out-of-plane and torsion angle methods for calculation of pseudorotation parameters revealed that the latter method is better suited to describe the internal coordinates of the non-equilateral five-membered ring. Inspection of the distribution of phase angles and puckering amplitudes lends additional support to the hypothesis that conformational interconversion of the familiar N and S type ring conformers is a process of hindered pseudorotation, proceeding through the O4′endo conformation (P = 90°) and maintaining a constant puckering amplitude. Both syn-anti distribution and preferred ranges of χ are correlated with furanose conformation in ribonucleosides; the distribution is also affected by the type of base, purines showing higher syn/anti ratios than pyrimidines. Three modes are observed for the backbone torsion angle δ(C4′–C5′); the most abundant rotamer is δ+, followed by δa. The δ− rotamer has so far been found only in S-type furanosides. Regressions based on existing or modified equations were used to express variations in internal coordinates in terms of the four parameters involved. As a consequence of its anomeric character, the glycosidic bond length can be described by a cyclic function of χ. Endocyclic bond angles' and torsion angles show small but systematic deviations from the pseudorotation equations derived for equilateral rings. Based on observed correlations with the four parameters, reasonably accurate coordinates for exocyclic atoms, including hydrogen atoms, could also be obtained. Coordinates for model β-D-furanoside fragments with preferred χ and δ orientations and variable pseudorotation parameters, covering a part of the N ⇌ S interconversion pathway, are presented. Their usefulness in future theoretical and experimental studies on nucleic acid conformations, both in the solid state and in solution, is discussed.
Comment on an Article by Aleanakian et al. Titled “Effectiveness, Safety, and Predictive Potential in Ultrasound‐Guided Stellate Ganglion Blockades (SGB) for the Treatment of Sympathetically Maintained Pain”

We read with immense interest the article by Aleanakian et al.1 about effectiveness, safety, and predictive potential of ultrasound-guided Stellate ganglion blockades (SGB) for the treatment of sympathetically maintained pain. We appreciate the exhaustive effort by authors to collect data of such long duration and conclude the factors which could help predict the effectiveness of SGB. However, we do have some queries about the methodology and results of this study.