Miracle-dz/UniFAR-FTUs huggingface dataset:
Goldilocks calcium and the mitochondrial respiratory chain: too much, too little, just right

Calcium (Ca2+) is a key regulator in diverse intracellular signaling pathways, and has long been implicated in metabolic control and mitochondrial function. Mitochondria can actively take up large amounts of Ca2+, thereby acting as important intracellular Ca2+ buffers and affecting cytosolic Ca2+ transients. Excessive mitochondrial matrix Ca2+ is known to be deleterious due to opening of the mitochondrial permeability transition pore (mPTP) and consequent membrane potential dissipation, leading to mitochondrial swelling, rupture, and cell death. Moderate Ca2+ within the organelle, on the other hand, can directly or indirectly activate mitochondrial matrix enzymes, possibly impacting on ATP production. Here, we aimed to determine in a quantitative manner if extra or intramitochondrial Ca2+ modulate oxidative phosphorylation in mouse liver mitochondria and intact hepatocyte cell lines. To do so, we monitored the effects of more modest versus supra-physiological increases in cytosolic and mitochondrial Ca2+ on oxygen consumption rates. Isolated mitochondria present increased respiratory control ratios (a measure of oxidative phosphorylation efficiency) when incubated with low (2.4 ± 0.6 μM) and medium (22.0 ± 2.4 μM) Ca2+ concentrations in the presence of complex I-linked substrates pyruvate plus malate and α-ketoglutarate, respectively, but not complex II-linked succinate. In intact cells, both low and high cytosolic Ca2+ led to decreased respiratory rates, while ideal rates were present under physiological conditions. High Ca2+ decreased mitochondrial respiration in a substrate-dependent manner, mediated by mPTP. Overall, our results uncover a Goldilocks effect of Ca2+ on liver mitochondria, with specific “just right” concentrations that activate oxidative phosphorylation.
Interneuronal network model of theta-nested fast oscillations predicts differential effects of heterogeneity, gap junctions and short term depression for hyperpolarizing versus shunting inhibition

Theta and gamma oscillations in the hippocampus have been hypothesized to play a role in the encoding and retrieval of memories. Recently, it was shown that an intrinsic fast gamma mechanism in medial entorhinal cortex can be recruited by optogenetic stimulation at theta frequencies, which can persist with fast excitatory synaptic transmission blocked, suggesting a contribution of interneuronal network gamma (ING). We calibrated the passive and active properties of a 100-neuron model network to capture the range of passive properties and frequency/current relationships of experimentally recorded PV+ neurons in the medial entorhinal cortex (mEC). The strength and probabilities of chemical and electrical synapses were also calibrated using paired recordings, as were the kinetics and short-term depression (STD) of the chemical synapses. Gap junctions that contribute a noticeable fraction of the input resistance were required for synchrony with hyperpolarizing inhibition; these networks exhibited theta-nested high frequencies (∼200 Hz) similar to the putative ING observed experimentally in the optogenetically-driven PV-ChR2 mice. With STD included in the model, fast oscillations were only observed before the peak of the theta drive, whereas without STD, they were observed symmetrically before and after the peak. Because hyperpolarizing synapses provide a synchronizing drive that contributes to robustness in the presence of heterogeneity, synchronization decreases as the hyperpolarizing inhibition becomes weaker. In contrast, networks with shunting inhibition required non-physiological levels of gap junctions to synchronize using conduction delays within the measured range; synaptic depression of shunting synapses facilitated fast oscillations, suggesting that shunting inhibition in mEC is desynchronizing. Author Summary Fast oscillations nested within slower oscillations have been hypothesized to play a role in the encoding and retrieval of memories by chunking information within each fast cycle; networks of parvalbumin positive inhibitory interneurons contribute to the generation of fast oscillations. We show that, in the entorhinal cortex, the intrinsic dynamical properties of these neurons are sufficiently heterogeneous that electrical synapses are likely required to synchronize fast oscillations. Moreover, synchrony likely requires the chemical synapses to have a reversal potential that is negative relative to the action potential threshold of individual neurons during these oscillations. We show that the range of slow phases that support a fast oscillation is controlled by short term synaptic depression. The precise phase locking of the fast oscillation within the slow oscillations is hypothesized to allow for multiplexing of information.
A Causal Role of Human Laryngeal Motor Cortex in 1 Speech Lexical Tone and Voicing Perception

To achieve categorical speech perception, listeners can actively reconstruct motor 20 gestures of the upcoming speech. This is supported by sensorimotor integration function of the dorsal pathway where the “internal models” of articulations implement top-down constraints on auditory speech analyses in the ventral pathway. Moreover, the motor engagement in speech perception is effector-specific, resembling the motor somatotopy during speech production. However, whether and how the laryngeal motor cortex (LMC), which controls the laryngeal muscles that regulate pitch contours and speech voicing, is also involved in speech perception remains largely 27 unknown. To address this question, this study applied transcranial magnetic 28 stimulation (TMS) upon the left or right LMC when participants performed 29 categorical perception tasks on Mandarin lexical tone (pitch contour contrast) or 30 consonant (voice onset time contrast) presented with or without noise. Results showed 31 that, inhibitory stimulation (repetitive TMS or continuous theta-burst stimulation) on 32 the LMC impaired both tone and consonant perception. Furthermore, TMS effects 33 were especially evident when syllables were masked by noise. These results reveal a 34 causal role of the LMC in speech perception that (1) it mirrors its distinctive functions 35 in controlling pitch and voicing during production and (2) it is upregulated and shifts 36 from a left-lateralized to a bilateral engagement in adverse listening conditions as a 37 means of compensation. This study thus provides new evidence to support the motor 38 theory of speech perception, and more generally, active perception and embodied 39 cognition.
Metabolite profiles across populations of Palmer amaranth (Amaranthus palmeri) highlight the specificity and inducibility of phytochemical response to glyphosate stress

Modifications of the phytochemical profile form a vital component of physiological stress adaptation in plants. However, the specificity and uniqueness of phytochemical changes with respect to the identity of stressors is less known. Here, we investigated the commonality and specificity of metabolic perturbations induced by a specific stressor – glyphosate, and a general stressor – drought, across multiple glyphosate-resistant (GR) and -susceptible (GS) biotypes of a dominant agricultural weed, Amaranthus palmeri. In the absence of stress, the native metabolite profile of GS- and GR-biotypes was similar, and amplification of the EPSPS gene in GR-biotypes did not translate to a higher abundance of downstream metabolites. Further, glyphosate treatment initially inhibited the shikimate pathway in both GS- and GR-biotypes, from which the GR-biotypes recovered, indicating inducibility in the functionalization of the EPSPS enzyme. The accumulation of phenylpropanoids produced downstream of the shikimate pathway, was higher in GR-biotypes than GS-biotypes, with a preferential accumulation of compounds with higher antioxidant potential. However, this increase was not observed in response to drought treatment, where the metabolic perturbations were pervasive but limited in magnitude compared to glyphosate stress. Overall, while native phytochemistry of A. palmeri was similar irrespective of the level of glyphosate susceptibility, the specific stressor, glyphosate, imparted metabolic perturbations that were localized but higher in magnitude, while the specificity of phytochemical response to the general stressor, drought, was minimal. Taken together, these results suggest that, at the metabolic level, the glyphosate resistance mechanism in A. palmeri is partly induced and specific to herbicide stress. SIGNIFICANCE STATEMENT Understanding changes in physiology, especially those related to secondary metabolites with adaptogenic functions, is imperative to decipher the basis of stress adaptation in plants. This study provides critical information on native and stress-induced phytochemical differences between multiple glyphosate-resistant and -susceptible weed biotypes, thus, shedding light on the metabolome-level orchestration of gene amplification-mediated glyphosate resistance mechanism in an economically devastating weed, Palmer amaranth (Amaranthus palmeri).
A Note on Baffle Orientation in Long Ponds

This paper assesses the general idea of implementing transversal baffles to improve hydraulic efficiency of rectangular ponds used in water and wastewater treatment processes. The paper concentrates on long ponds with the length-to-width ratio of 4:1. Three different scenarios of plain (baffle-less) pond and ponds with four transversal and two longitudinal baffles were considered. A two dimensional Computational Fluid Dynamics (CFD) conservative tracer study was performed. Results showed that the longitudinal layout of the baffles yielded to a hydraulic regime closer to the plug-flow condition, while application of limited number of transverse baffles in long ponds showed an adverse effect on the overall hydraulic performance. Such baffles layout yielded to increased dispersion, as well as comparable dead zones in comparison with the plain pond. A three dimensional analysis was also conducted to evaluate the effect of volumetric dispersion, which yielded to the same results. Possible reasons for this phenomenon were discussed. Results suggest that application of limited number of transverse baffles in long ponds needs extra consideration.
Pro187Ser Polymorphism of NAD(P)H:quinone oxidoreductase 1 and Prognosis of Non-small Cell Lung Cancer after Radiation Therapy

Departments of Radiation Oncology and Medical Oncology, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Korea Department of Microbiology, College of Medicine, Inha University, Incheon, Korea Departments of Preventive Medicine and Radiation Oncology, College of Medicine, Seoul National University, Seoul, Korea DNA Link Inc., Seoul, Korea *Correspondence: Eun Kyung Choi, e-mail: ekchoi@amc.seoul. kr
Digital Dynamics and Types of Industry Convergence: The Evolution of the Handheld Computers Market

One recurrent theme in the discussion about the salient features of the digital economy is the claim that industries like telecommunications, computing, and entertainment are converging. While the notion of industry convergence of industry convergence is often used to characterize industrial dynamics, it is seldom clearly defined. The paper develops a taxonomy that allows for the identification and disentanglement of different drivers of industry convergence. The taxonomy is applied to an analysis of the handheld computer industry. It is shown that different types of industry convergence shaped corporate strategy and competitive dynamics in this particular industry, making the industry a particularly interesting case for studying convergence.
The Distributional Impact of the Minimum Wage ∗

We develop a general equilibrium framework with worker heterogeneity, monopsony power, and putty-clay frictions in order to study the distributional impact of large changes in the minimum wage. In the long run, we find that a high minimum wage has perverse distributional impacts in that it reduces the employment, income, and welfare of precisely the low-income workers it was meant to help. However, these long-run consequences take twenty years to fully materialize because firms slowly adjust the labor intensity of their capital stock. We also study the long-run impacts of alternative transfer programs, such as the earned-income tax credit, and find they are much more effective at improving outcomes for workers at the bottom of the wage distribution. In this context, a modest increase in the minimum wage is beneficial because it prevents firms from lowering the pre-transfer wages they pay to workers.
The Associations between Early Maternal Language Use and School Readiness among Young Children of Asian and Hispanic Immigrant Mothers in the United States

This study examined how early maternal language use was associated with school readiness at kindergarten entry among children of Asian or Hispanic immigrant mothers in the United States. Using a nationally representative sample from the Early Childhood Longitudinal Study-Birth Cohort (ECLS-B; N ≈ 1,500), this study estimates multivariate regression models to address each research question. This study finds generally advantages of maternal use of English and bilingualism for children’s expressive language in both Asian and Hispanic groups and for children’s pro-social behavior in the Asian group. It also finds that longer residency in the U.S. is associated with higher levels of approaches to learning for children of bilingual Asian mothers and lower levels of behavior problems for children of bilingual Hispanic mothers. Based on the findings, social work implications for the healthy development of young children of immigrants were discussed.
Thriving despite Parental Physical Abuse in Adolescence: A Two-Wave Latent Transition Analysis on Hedonic and Eudaimonic Violence-Resilience Outcome Indicators

Internationally, about 25% of all children experience physical abuse by their parents. Despite the numerous odds against them, about 30% of adolescents who have experienced even the most serious forms of physical abuse by their parents escape the vicious family violence cycle. In this study, we analyzed longitudinally the data from a sample of N = 1767 seventh-grade high school students in Switzerland on physical abuse by their parents. We did this by conducting an online questionnaire twice within the school year. We found that in our sample, about 30% of the participating adolescents’ parents had physically abused them. We considered violence resilience a multi-systemic construct that included the absence of psychopathology on one hand and both forms of well-being (psychological and subjective) on the other. Our latent construct included both feeling good (hedonic indicators, such as high levels of self-esteem and low levels of depression/anxiety and dissociation) and doing well (eudaimonic indicators, such as high levels of self-determination and self-efficacy as well as low levels of aggression toward peers). By applying a person-oriented analytical approach via latent transition analysis with a sub-sample of students who experienced physical abuse (nw2 = 523), we identified and compared longitudinally four distinct violence-resilience patterns and their respective trajectories. By applying to the field of resilience, one of the most compelling insights of well-being research (Deci & Ryan, 2001), we identified violence resilience as a complex, multidimensional latent construct that concerns hedonic and eudaimonic well-being and is not solely based on terms of psychopathology.
UNIVERSDIDADE DE SÃO PAULO INSTITUTO DE BIOCIÊNCIAS PROGRAMA DE PÓS-GRADUAÇÃO EM CIÊNCIAS BIOLÓGICAS (BOTÂNICA)

The C 4 cycle and crassulacean acid metabolism (CAM) are two common carbon concentrating mechanisms (CCM) in vascular plants. They have biochemical similarities, but represent very different ecological adaptations, as a result of evolutionary, regulatory and structural differences. It was believed they were incompatible to occur in a single organism, but the genus Portulaca challenges this assumption, as it presents intermediate C 3 -C 4 and C 4 species capable of switching to CAM according to water availability. However, the genetic and regulatory mechanisms that enable this rare photosynthetic adaptation to occur are still poorly understood. Therefore, the aim of this doctoral thesis was to investigate the C 4 to CAM transition in P. oleracea from a physiological and molecular point of view. After a brief introduction to the subject, chapter I contextualizes and proposes the species as a model for studying the C 4 -CAM transition. Chapter II characterized the central genetic machinery involved in both CCMs in P. oleracea using transcriptome data associated with phylogenetic and physiological analyses. Chapter III explored the morphophysiological plasticity of the species, characterizing CAM in different subspecies originated in different parts of the world. Chapter IV discusses the best optimized molecular strategies and protocols enabling the use of P. oleracea as a C 4 CAM model. Finally, Chapter V characterizes the molecular and hormonal signaling during the C 4 -to-CAM transition and reversion and brings insights into the influence of the circadian clock on both CCMs' functioning. In general, and most importantly in the global context of climate change, this work aimed to emphasize that C 4 and CAM not only represent interesting physiological adaptations from both a functional and evolutionary point of view, but are also important mechanisms for the development of society, as they occur separately in cultivars used in food production and biofuels. Thus, this work provides information that makes it possible to explore the complexity of Portulaca as a blueprint for future development via genetic engineering of cultivars that can intercalate C 4 and CAM in a single organism according to the availability of resources in the environment.
Latent heat must be visible in climate communications

Anthropogenic forcing is driving energy accumulation in the Earth system, including increases in the sensible heat content of the atmosphere, as measured by dry‐bulb temperature—the metric that is almost universally used for communications about climate change. The atmosphere is also moistening, though, representing an accumulation of latent heat, which is partly concealed by dry‐bulb temperature trends. We highlight that, consistent with basic theory, latent heat gains are outpacing sensible heat gains over about half of the Earth's surface. The difference is largest in the tropics, where global “hotspots” of total heat accumulation are located, and where regional disparities in heating rates are very poorly represented by dry‐bulb temperatures. Including latent heat in climate‐change metrics captures this heat accumulation and therefore improves adaptation‐relevant understanding of the extreme humid heat and precipitation hazards that threaten these latitudes so acutely. For example, irrigation can lower peak dry‐bulb temperatures, but amplify latent heat content by a larger margin, intensifying dangerous heat stress. Based on a review of the research literature, our Perspective therefore calls for routine use of equivalent temperature, a measure that expresses the combined sensible and latent heat content of the atmosphere in the familiar units of °C or K. We recognize that dry‐bulb air temperature must remain a key indicator of the atmospheric state, not least for the many sectors that are sensitive to sensible heat transfer. However, we assert here that more widespread use of equivalent temperature could improve process understanding, public messaging, and adaptation to climate change.
Deformability Parameters of Varved Clays From the Iłów (Central Poland) Area Based on the Selected Field Tests

Abstract This publication presents the results of research carried out for the ice-dammed clays of the Iłów region, formed during Vistula glaciation. Pressuremeter tests, dilatometer tests and static probes were made. The tests were performed on the study site in Piskorzec near Iłów. In this region, ice-dammed clays are present almost from the land surface reaching the thickness of about 11 m. This site is the westernmost experimental site of clays of the “Warsaw Ice-Dammed Lake” among those presented in the literature. Research and their analysis showed differences in deformability due to the test procedure in connection with the structure of varved clays. Pressuremeter test, even though it is the most time consuming and challenging among the tests performed, allows the most complete characteristics of deformability of varved clays to be obtained. Vertical profile of clays being studied appears to be fairly homogeneous in terms of mechanical properties. Nevertheless, some parts of the profile clearly differ from the average values. This indicates the rate of post sedimentary changes varied in different parts of research profile. The data obtained are consistent with the values for ice-dammed clays from Radzymin and Sochaczew areas. Comparison of the engineering properties of varved clays to other experimental sites points to their similar geological history. It confirms that the experimental sites belong to one ice-dammed lake covering the areas of the Warsaw Basin.
Artemether inhibits proliferation, invasion and migration of hepatocellular carcinoma cells via targeting of CYP2J2

Artemether, a natural derivative of artemisinin, serves an antitumor role in numerous types of cancer. However, the role and mechanism of action of artemether in hepatocellular carcinoma (HCC) has remained elusive. The present study aimed to investigate whether artemether is able to inhibit the proliferation, invasion and migration of HCC cells by targeting cytochrome P450 family 2 subfamily J member 2 (CYP2J2). Cell Counting Kit-8 (CCK-8) and colony-formation assays were used to examine cell viability. Wound-healing and Transwell assays were used to evaluate the cell invasion and migration ability. The expression levels of the epithelial-mesenchymal transition-related proteins E-cadherin, N-cadherin and vimentin were detected via western blot analysis. To determine the mechanism of the inhibitory effect of artemether on HCC, CYP2J2 was overexpressed and its expression in cells treated with artemether was confirmed using reverse transcription-quantitative PCR and western blot analysis. The effects of artemether on the viability, proliferation and migration of HCC cells overexpressing CYP2J2 were detected using CCK-8, colony-formation, wound-healing and Transwell assays, respectively. Artemether was demonstrated to exert a significant inhibitory effect on the proliferation, invasion and migration of HCC cells. Furthermore, artemether also inhibited CYP2J2 expression in Hep3B2.1-7 cells and CYP2J2 overexpression reversed the inhibitory effect of artemether on the proliferation, invasion and migration of HCC cells. Overall, these results indicated that artemether may inhibit HCC cell proliferation, invasion and migration via targeting CYP2J2. These findings may provide potential targets for future HCC therapeutics.