Miracle-dz/UniFAR-FTUs huggingface dataset:
Megamitochondria formation ‐ physiology and pathology

Mitochondria undergo structural changes simultaneously with their functional changes in both physiological and pathological conditions. These structural changes of mitochondria are classified into two categories: simple swelling and the formation of megamitochondria (MG). Data have been accumulated to indicate that free radicals play a crucial role in the mechanism of the MG formation induced by various experimental conditions which are apparently various. These include ethanol‐, chloramphenicol‐ and hydrazine‐induced MG formation. Involvement of free radicals in the mechanism of MG formation is showed by the fact that MG formation is successfully suppressed by free radical scavengers such as α‐tocopherol, coenzyme Q10, and 4‐OH‐TEMPO. Detailed mechanisms and pathophysiological meanings of MG formation still remain to be investigated. However, a body of evidence strongly suggests that enormous changes in physicochemical and biochemical properties of the mitochondrial membranes during MG formation take place and these changes are favorable for membrane fusion. A recent report showed that continous exposure of cells with MG to free radicals induces apoptosis, finding which suggests that MG formation is an adaptative process to unfavorable environments at the level of intracellular organelles. Mitochondria try to decrease intracellular reactive oxygen species (ROS) levels by decreasing the consume of oxygen via MG formation. If mitochondria succeed to suppress intracellular ROS levels, MG return to normal both structurally and functionally, and they restore the ability to actively synthesize ATP. If cells are additionally exposed to excess amounts of free radicals, MG become swollen, membrane potential of mitochondria (ΔΨm) decreases, cytochrome c is released from mitochondria, leading to activation of caspases and apoptosis is induced.
Statistical Power of Expression Quantitative Trait Loci for Mapping of Complex Trait Loci in Natural Populations

A number of recent genomewide surveys have found numerous QTL for gene expression, often with intermediate to high heritability values. As a result, there is currently a great deal of interest in genetical genomics—that is, the combination of genomewide expression data and molecular marker data to elucidate the genetics of complex traits. To date, most genetical genomics studies have focused on generating candidate genes for previously known trait loci or have otherwise leveraged existing knowledge about trait-related genes. The purpose of this study is to explore the potential for genetical genomics approaches in the context of genomewide scans for complex trait loci. I explore the expected strength of association between expression-level traits and a clinical trait, as a function of the underlying genetic model in natural populations. I give calculations of statistical power for detecting differential expression between affected and unaffected individuals. I model both reactive and causative expression-level traits with both additive and multiplicative multilocus models for the relationship between phenotype and genotype and explore a variety of assumptions about dominance, number of segregating loci, and other parameters. There are two key results. If a transcript is causative for the disease (in the sense that disease risk depends directly on transcript level), then the power to detect association between transcript and disease is quite good. Sample sizes on the order of 100 are sufficient for 80% power. On the other hand, if the transcript is reactive to a disease locus, then the correlation between expression-level traits and disease is low unless the expression-level trait shares several causative loci with the disease—that is, the expression-level trait itself is a complex trait. Thus, there is a trade-off between the power to show association between a reactive expression-level trait and the clinical trait of interest and the power to map expression-level QTL (eQTL) for that expression-level trait. Gene expression-level traits that are most strongly correlated with the clinical trait will themselves be complex traits and therefore often hard to map. Likewise, the expression-level traits that are easiest to map will tend to have a low correlation with the clinical trait. These results show some fundamental principles for understanding power in eQTL-based mapping studies.
Acetylation of Androgen Receptor Enhances Coactivator Binding and Promotes Prostate Cancer Cell Growth

ABSTRACT Modification by acetylation occurs at ε-amino lysine residues of histones and transcription factors. Unlike phosphorylation, a direct link between transcription factor acetylation and cellular growth or apoptosis has not been established. We show that the nuclear androgen receptor (AR), a DNA-binding transcriptional regulator, is acetylated in vivo. The acetylation of the AR is induced by ligand dihydrotestosterone and by histone deacetylase (HDAC) inhibitors in living cells. Direct AR acetylation augmented p300 binding in vitro. Constructs mimicking neutral polar substitution acetylation (ARK630Q, ARK630T) enhanced p300 binding and reduced N-CoR/HDAC/Smad3 corepressor binding, whereas charged residue substitution (ARK630R) reduced p300 binding and enhanced corepressor binding. The AR acetylation mimics promoted cell survival and growth of prostate cancer cells in soft agar and in nude mice and augmented transcription of a subset of growth control target gene promoters. Thus, transcription factor acetylation regulates coactivator/corepressor complex binding, altering expression of specific growth control genes to promote aberrant cellular growth in vivo.
Effects of the Inductive Hardening Process on the Martensitic Structure of a 50CrMo4 Steel

Abstract This study focuses on the influence of a fast heat treatment, as occurring with induction heating processes, on the microstructural features, and their effect on the mechanical properties of a 50CrMo4 steel. To this end, three different heating rates (1 K/s, 10 K/s, and 100 K/s) and three different austenitizing temperatures (950 °C, 1000 °C, 1050 °C) were applied to a ferritic-pearlitic steel. After quenching, the resulting martensitic microstructures were investigated and compared to a conventional furnace heat treating sequence using electron back scattered diffraction (EBSD). Thus, the effect of variable heating rates during austenitization on the resulting martensitic microstructure, including the evaluation of packet and block sizes and orientations, was analyzed. Through the investigations of this work, it could be shown, that the adaption of the Kurdjumov-Sachs (K-S) variants is changing with the prior heat treatment. The occurrence of all 24 K-S variants in the same intensity increases and the misorientation angle across a martensite block decrease with higher austenitizing temperatures, despite fast heating rates. Therefore, it is suggested, that the austenitizing temperature has more impact on the martensitic structure than the heating rate.
Use of Absorbable Poly (D,L) Lactic Acid Plates in Cranial-Vault Remodeling: Presentation of the First Case and Lessons Learned about Its Use

Objective To present the first clinical use of a new bioabsorbable material, poly (D,L) lactic acid (PDLLA), in pediatric cranial-vault remodeling procedures. This discussion will highlight the benefits and detriments of PDLLA in comparison with currently used absorbable plating systems. Design This was a case study documenting the first North American case in which PDLLA was used to treat craniosynostosis. Materials and Methods Evaluation of pure PDLLA, a copolymer product of the mixture of poly L-lactic acid and its D-isomer, was used in an 8-month-old boy with a severe phenotypic expression of sagittal craniosynostosis. No signs of elevated intracranial pressure were present, and the neurological examination did not show impairments. Total cranial-vault remodeling with the “hung-span” technique was performed. The Resorb X system, containing 2.2-mm screws and 0.6- to 1-mm-thick plates, was used to stabilize the reconstructed cranial vault. Results No surgical complications occurred. The preoperative cranial index measured 62. The scaphocephalic appearance of the skull was eliminated, and the cranial index was normalized to 77. The screws and plates were less palpable than other plating systems. Twelve months postoperatively, none of the plates and screws were identifiable by external palpation. Conclusion Resorb X has been successfully used in the treatment of sagittal craniosynostosis. Its rapid rate of resorption and lower profile make it an advantageous system for pediatric skull reconstruction. This represents the first use of this product in the United States for any pathology.
Detection of Encrypted Data Based on Support Vector Data Description

Data encryption has been widely used. It is important to detect encrypted data. We present a method for detection of encrypted data based on the Support Vector Data Description (SVDD) algorithm. The SVDD is a single class, non-parametric approach for modeling the support of a distribution. We apply the SVDD techniques for detection of encrypted data. Experimental results show that the SVDD can be adopted as an effective tool for detection of encrypted data.
Modelling Word Similarity: an Evaluation of Automatic Synonymy Extraction Algorithms.

Vector-based models of lexical semantics retrieve semantically related words automatically from large corpora by exploiting the property that words with a similar meaning tend to occur in similar contexts. Despite their increasing popularity, it is unclear which kind of semantic similarity they actually capture and for which kind of words. In this paper, we use three vector-based models to retrieve semantically related words for a set of Dutch nouns and we analyse whether three linguistic properties of the nouns influence the results. In particular, we compare results from a dependency-based model with those from a 1st and 2nd order bag-of-words model and we examine the effect of the nouns frequency, semantic speficity and semantic class. We find that all three models find more synonyms for high-frequency nouns and those belonging to abstract semantic classses. Semantic specificty does not have a clear influence.
Metal Tolerance Protein 8 Mediates Manganese Homeostasis and Iron Reallocation during Seed Development and Germination1[OPEN]

MTP8 mediates metal homeostasis and seed vigor by cell type-specific vacuolar loading of Mn and Fe in developing embryos and during seed imbibition. Metal accumulation in seeds is a prerequisite for germination and establishment of plants but also for micronutrient delivery to humans. To investigate metal transport processes and their interactions in seeds, we focused on METAL TOLERANCE PROTEIN8 (MTP8), a tonoplast transporter of the manganese (Mn) subclade of cation diffusion facilitators, which in Arabidopsis (Arabidopsis thaliana) is expressed in embryos of seeds. The x-ray fluorescence imaging showed that expression of MTP8 was responsible for Mn localization in subepidermal cells on the abaxial side of the cotyledons and in cortical cells of the hypocotyl. Accordingly, under low Mn availability, MTP8 increased seed stores of Mn, required for efficient seed germination. In mutant embryos lacking expression of VACUOLAR IRON TRANSPORTER1 (VIT1), MTP8 built up iron (Fe) hotspots in MTP8-expressing cells types, suggesting that MTP8 transports Fe in addition to Mn. In mtp8 vit1 double mutant seeds, Mn and Fe were distributed in all cell types of the embryo. An Fe transport function of MTP8 was confirmed by its ability to complement Fe hypersensitivity of a yeast mutant defective in vacuolar Fe transport. Imbibing mtp8-1 mutant seeds in the presence of Mn or subjecting seeds to wet-dry cycles showed that MTP8 conferred Mn tolerance. During germination, MTP8 promoted reallocation of Fe from the vasculature. These results indicate that cell type-specific accumulation of Mn and Fe in seeds depends on MTP8 and that this transporter plays an important role in the generation of seed metal stores as well as for metal homeostasis and germination efficiency under challenging environmental conditions.
Extracellular signal‐regulated protein kinase in human intractable epilepsy

Extracellular signal‐regulated kinases (ERK) such as ERK1 [p44 mitogen‐activated protein kinase (MAPK)] and ERK2 (p42 MAPK) are activated in the central nervous system under physiological and pathological conditions such as ischemia and epilepsy. Our aim is to investigate ERK1, ERK2, and phosphorylated ERK (p‐ERK) (Thr202/Tyr 204) expression in the temporal lobe of patients with intractable epilepsy (IE) and to explore its possible role of ERK in it. Tissue samples from temporal neocortices of 40 patients who had surgery for IE were used to detect ERK1, ERK2, and p‐ERK (Thr 202/Tyr 204) expression through immunohistochemistry and western blot. We compared these tissues against 17 histological normal temporal lobes from head‐traumat patients. ERK1, ERK2, and p‐ERK in IE were significantly higher than those in the controls. They were mainly expressed in the cytoplasm of neurons and glial cells. There was also increased detection of p‐ERK in the gliotic cortex of IE compared with the non‐gliotic cortex. These findings were consistently observed in western blot and immunohistochemistry techniques. ERK expression in patients with IE was significantly increased compared with the controls. This suggested a probable role of ERK in the pathogenesis of IE.
Stability of nuclear DNA content among divergent and isolated populations of Fraser fir

Fraser fir (Abies fraseri (Pursh) Poir. ) is an endemic species consisting of six major disjunct populations in the Appalachian Mountains, U.S.A. Nuclear DNA content was measured with laser flow cytometry to determine if genome size differences could be detected among the disjunct populations of Fraser fir and its close relatives, balsam fir (Abies balsamea (L.) Mill. ) and Canaan fir (A. balsamea var. phanerolepsis Fern.). The mean DNA content for Fraser fir was 17.2 pg/C, which was similar to the two related fir species. There were no significant differences among disjunct Fraser-fir populations. Mean DNA content differences for fir species in the southern Appalachian Mountains were similar even with speciation events (7000 B.P.) and subsequent population isolation. In the absence of polyploidy or large chromosomal rearrangements, genome size changes in conifers occur on a broad evolutionary time scale.Key words: conifers, gymnosperm, C-values, nuclear genome, Abies fraseri.
β-Amyloid Treatment Sensitizes Mice to Amphetamine-Induced Locomotion but Reduces Response to Caffeine

Backgroud: Psychosis frequently occurs in Alzheimer’s disease (AD), being associated with more severe cognitive decline, but the underlying mechanisms are unknown. Objective: To investigate the effect of centrally administered β-amyloid peptide, a model for AD, in the locomotor response to amphetamine, caffeine and MK-801, which are psychoactive drugs related to neurochemical changes occurring in psychosis. Methods: Mice were intracerebroventricularly injected with β-amyloid (25–35), and after 1 week they were tested in the passive avoidance, spontaneous alternation and locomotor tasks. Results: Besides impaired performance in inhibitory avoidance and spontaneous alternation tasks, β-amyloid-treated mice showed increased spontaneous locomotion, augmented response to amphetamine (1.5 mg/kg), blunted response to caffeine (30 mg/kg) and no difference in MK-801 (0.25 mg/kg)-induced locomotor activation when compared to its respective control. Conclusion: These results are compatible with the hypothesis that β-amyloid peptide may predispose to psychotic symptoms of AD by increasing sensitivity of the dopaminergic system, possibly related to a decreased adenosinergic inhibitory tone.
BOLD, sweat and fears: fMRI and skin conductance distinguish facial fear signals

It is not known how the brain and autonomic systems interact during perception of facial signals of danger. We recorded blood-oxygen-level-dependent (BOLD) activity using fMRI and simultaneous skin conductance measures of autonomic arousal in healthy subjects. Distinct response profiles were elicited for fear (enhanced arousal with amygdala activity), anger (rapid onset, slow recovery arousal responses with anterior cingulate) and disgust (delayed arousal responses with insula and basal ganglia activity). The findings suggest that fear, anger and disgust perception involves specific interactions in the neural arousal systems for emotion and motivation.
Near-Optimal Separators in String Graphs

Let G be a string graph (an intersection graph of continuous arcs in the plane) with m edges. Fox and Pach proved that G has a separator consisting of $O(m^{3/4}\sqrt{\log m})$ vertices, and they conjectured that the bound of $O(\sqrt m)$ actually holds. We obtain separators with $O(\sqrt m \,\log m)$ vertices.
Sacrificial Structure for Effective Sapphire Substrate Liftoff Based on Photoelectrochemical Etching

The photoelectrochemical (PEC) liftoff results and the performances of fabricated vertical light-emitting diodes (LEDs) among four samples of different PEC etching sacrificial structures are compared. With a dopant-graded n-GaN sacrificial layer, the PEC liftoff time is decreased. With an n-AlGaN etching-stop layer, the roughness of PEC-etching surface is significantly reduced for simplifying the following device process. Illuminated by an ultraviolet LED array at 365 nm in emission wavelength, the PEC liftoff of a 2-in wafer with device isolation can be completed in 25 min. The performances of the fabricated vertical LEDs with different sacrificial structures are similar.
Online Channel Allocation for Full-Duplex Device-to-Device Communications

Full-duplex device-to-device (D2D) communications over cellular networks is a promising solution for maximizing wireless spectral efficiency. However, in practice, due to the unpredictable arrival of D2D users, the base station (BS) must smartly allocate suitable channels to arriving D2D pairs. In this paper, the problem of dynamic channel allocation is studied for full-duplex D2D networks. In particular, the goal of the proposed approach is to maximize the system sum-rate under complete uncertainty on the arrival process of D2D users. To solve this problem, a novel approach based on an online weighted bipartite matching is proposed. To find the desired solution of the channel allocation problem, a greedy online algorithm is developed to enable the BS to decide on the channel assignment for each D2D pair, without knowing any prior information on future D2D arrivals. For an illustrative case study, upper and lower bounds on the competitive ratio that compares the performance of the proposed online algorithm to that of an offline algorithm are derived. Simulation results show that the proposed online algorithm can achieve a near- optimal sum-rate with an optimality gap that is no higher than 8.3% compared to the offline, optimal solution that has complete knowledge of the system.
High Throughput Gene Expression Analysis Identifies Reliable Expression Markers of Human Corneal Endothelial Cells

Considerable interest has been generated for the development of suitable corneal endothelial graft alternatives through cell-tissue engineering, which can potentially alleviate the shortage of corneal transplant material. The advent of less invasive suture-less key-hole surgery options such as Descemet’s Stripping Endothelial Keratoplasty (DSEK) and Descemet’s Membrane Endothelial Keratoplasty (DMEK), which involve transplantation of solely the endothelial layer instead of full thickness cornea, provide further impetus for the development of alternative endothelial grafts for clinical applications. A major challenge for this endeavor is the lack of specific markers for this cell type. To identify genes that reliably mark corneal endothelial cells (CECs) in vivo and in vitro, we performed RNA-sequencing on freshly isolated human CECs (from both young and old donors), CEC cultures, and corneal stroma. Gene expression of these corneal cell types was also compared to that of other human tissue types. Based on high throughput comparative gene expression analysis, we identified a panel of markers that are: i) highly expressed in CECs from both young donors and old donors; ii) expressed in CECs in vivo and in vitro; and iii) not expressed in corneal stroma keratocytes and the activated corneal stroma fibroblasts. These were SLC4A11, COL8A2 and CYYR1. The use of this panel of genes in combination reliably ascertains the identity of the CEC cell type.
A framework for the observer design for networked control systems

This paper provides a general framework for the observer design for networked control systems (NCS) affected by disturbances, via an emulation-like approach. The proposed model formulation allows us to consider various static and dynamic time-scheduling protocols, in-network processing implementations and encompasses sampled-data systems as a particular case. Provided that the continuous-time observer is robust to measurement errors (in an appropriate sense) we derive bounds on the maximum allowable transmission interval (MATI) that ensure the convergence of observation errors under network-induced communication constraints. The stability analysis is trajectory-based and utilizes small-gain arguments. It has to be emphasized that this paper also furnishes new tools for the observer design for sampled-data systems. Various observers can be combined and used within our approach to obtain estimators for NCS.
Separation of solids in the surface-layers of solutions and ‘suspensions’ (observations on surface-membranes, bubbles, emulsions, and mechanical coagulation).—Preliminary account

In a paper published in Du Bois Reymond’s ‘Archiv für Anat. und Physiologie’ in 1894, I showed that mere agitation of various proteid solutions brought about a separation of some of their contained proteid in the form of fibrous or membrano-fibrous solids, and that it was possible in this way to coagulate and remove the whole of the proteid from solutions of egg-albumin. It was proved also that these de-solutions and coagulations of proteid were not due to the action of enzymes, heat, or surface evaporation, and were not appreciably affected by the nature of the gas in contact with the liquid or of the vessel in which the agitation was effected. A prolonged series of further experiments, undertaken with a view of ascertaining the precise cause of this phenomenon, has led me to the discovery of an important, but hitherto unnoticed physical fact:—namely, that, quite apart from evaporation, solid or highly viscous coatings are spontaneously, and more or less rapidly formed on the free surfaces of all proteid solutions.