Miracle-dz/UniFAR-FTUs huggingface dataset:
Interplay of Chimeric Mating-Type Loci Impairs Fertility Rescue and Accounts for Intra-Strain Variability in Zygosaccharomyces rouxii Interspecies Hybrid ATCC42981

The pre-whole genome duplication (WGD) Zygosaccharomyces clade comprises several allodiploid strain/species with industrially interesting traits. The salt-tolerant yeast ATCC42981 is a sterile and allodiploid strain which contains two subgenomes, one of them resembling the haploid parental species Z. rouxii. Recently, different mating-type-like (MTL) loci repertoires were reported for ATCC42981 and the Japanese strain JCM22060, which are considered two stocks of the same strain. MTL reconstruction by direct sequencing approach is challenging due to gene redundancy, structure complexities, and allodiploid nature of ATCC42981. Here, DBG2OLC and MaSuRCA hybrid de novo assemblies of ONT and Illumina reads were combined with in vitro long PCR to definitively solve these incongruences. ATCC42981 exhibits several chimeric MTL loci resulting from reciprocal translocation between parental haplotypes and retains two MATa/MATα expression loci, in contrast to MATα in JCM22060. Consistently to these reconstructions, JCM22060, but not ATCC42981, undergoes mating and meiosis. To ascertain whether the damage of one allele at the MAT locus regains the complete sexual cycle in ATCC42981, we removed the MATα expressed locus by gene deletion. The resulting MATa/- hemizygous mutants did not show any evidence of sporulation, as well as of self- and out-crossing fertility, probably because incomplete silencing at the chimeric HMLα cassette masks the loss of heterozygosity at the MAT locus. We also found that MATα deletion switched off a2 transcription, an activator of a-specific genes in pre-WGD species. These findings suggest that regulatory scheme of cell identity needs to be further investigated in Z. rouxii protoploid yeast.
OTA Measurement for IoT Wireless Device Performance Evaluation: Challenges and Solutions

The explosion of applications of Internet of Things (IoT) wireless devices urgently requires over-the-air (OTA) performance evaluations. However, the challenges mainly due to the fact that the ubiquitous IoT device applications have made it necessary for OTA measurements to be operated in accurate, fast, and cost-effective ways. This paper proposes a series of solutions for improving the standard OTA measurements to meet the IoT OTA requirements. For single-input single-output (SISO) terminals, three test techniques are introduced for speeding up their total isotropic sensitivity tests and improving the test accuracy. For IoT multi-input multioutput (MIMO) devices, the radiated two-stage (RTS) method is introduced. The detailed theories are described mathematically, including the pattern measurement error elimination and the inverse matrix auto-solving. The advantages of the RTS on MIMO system diagnosis are outlined. Besides, a smart test system was introduced, which is suitable for a general office building. Both SISO and MIMO can be conducted in this chamber, resulting in great cost saving. Thus, with innovations on hardware and methodologies, the OTA evaluations can be accommodated and helpful for the IoT industry.
Routing Algorithm Based on Trajectory Prediction in Opportunistic Networks

Due to the dynamic change of the opportunistic network topology and the lack of stable information transmission paths between nodes, the traditional topology-based routing algorithm cannot achieve the desired routing performance. To address of this problem, this paper proposes a routing algorithm based on trajectory prediction (RATP). The routing protocol based on trajectory prediction can efficiently and quickly adapt to the network link quality instability and the dynamic changes of network topology. RATP algorithm constructs a node mobility model by analyzing the historical mobility characteristics of the nodes. According to the node prediction information, the metric value of the candidate node is calculated, and the node with the smaller metric value is selected as the data forwarding node, which can effectively reduce the packet loss rate and avoids excessive consumption. Simulation results show that compared with other algorithms, the proposed algorithm has higher data delivery ratio, and end-to-end data delay and routing overhead are significantly reduced.
Beamformer Optimization for the Full-Duplex AF Relay Wiretap Channels

We consider optimal beamforming (BF) for the multiantenna full-duplex (FD) amplify-and-forward relay that maximizes the secrecy rate in the relay eavesdropper channel. We first show that zero forcing condition (ZFC) with no self-interference from the loop-back channel at the FD relay is the necessary condition for finding the optimal beamformer. Then, we provide an optimization method to locate the best pair among the ZFC beamformers. Through some simulations, we evaluate and compare the performances of the proposed optimal zero forcing BF scheme and a reference BF scheme.
Effects of Self-Enhancement on Eye Movements During Reading

Previous studies show that readers’ eye movements are influenced by text properties and readers’ personal cognitive characteristics. In the current study, we further show that readers’ eye movements are influenced by a social motivation of self-enhancement. We asked participants to silently read sentences that describe self or others with positive or negative traits while their eyes were monitored. First-fixation duration and gaze duration were longer when positive words were used to describe self than to describe others, but there was no such effect for negative words. These results suggest that eye movements can be influenced by the motivation of self-enhancement in addition to various stimuli features and cognitive factors. This finding indicates that the eye movement methodology can potentially be used to study implicit social cognition.
Molecular Profiling of Druggable Targets in Clear Cell Renal Cell Carcinoma Through Targeted RNA Sequencing

Clear cell renal cell carcinoma (ccRCC) comprises more than 80% of all renal cancers and when metastasized leads to a 5-year survival rate of only 10%. The high rate of therapy failure and resistance development calls for reliable methods that provide information on the actionable biological pathways and predict optimal treatment protocols for individual patients. We here applied targeted RNA sequencing (t/RNA-NGS) using single molecule Molecular Inversion Probes on tumor nephrectomy samples of five ccRCC patients, comparing tumor with healthy kidney tissues. Transcriptome profiling focused on expression of genes with involvement in ccRCC biology that can be targeted with clinically available drugs. Results confirm high expression of vascular endothelial growth factor-A (VEGF-A) in tumor tissue relative to healthy-appearing kidney, in line with the angiogenic nature of ccRCC. PDGFRα and KIT, targets of the multi-kinase inhibitor sunitinib which is one of the current choices of first-line drug in metastasized ccRCC patients, were expressed at relatively low levels in tumor tissues, whereas significantly increased in normal kidney. Of all measured druggable tyrosine kinases, MET, AXL, or EGFR were expressed at higher levels in tumors than in normal kidney tissues, although intertumor differences were observed. Using cancer cell lines we show that t/RNA-NGS gene expression profiles can be used to predict in vitro sensitivity to targeted drugs. In conclusion, t/RNA-NGS analysis may provide insights into the (druggable) molecular make-up of individual renal cancers, and may guide personalized therapy of renal cell cancers.
IGF1 Gene Therapy Modifies Microglia in the Striatum of Senile Rats

Microglial cells become dystrophic with aging; this phenotypic alteration contributes to basal central nervous system (CNS) neuroinflammation being a risk factor for age related neurodegenerative diseases. In previous studies we have observed that insulin like growth factor 1 (IGF1) gene therapy is a feasible approach to target brain cells, and that is effective to modify inflammatory response in vitro and to ameliorate cognitive or motor deficits in vivo. Based on these findings, the main aim of the present study is to investigate the effect of IGF1 gene therapy on microglia distribution and morphology in the senile rat. We found that IGF1 therapy leads to a region-specific modification of aged microglia population.
An Efficient Memory Partitioning Approach for Multi-Pattern Data Access via Data Reuse

Memory bandwidth has become a bottleneck that impedes performance improvement during the parallelism optimization of the datapath. Memory partitioning is a practical approach to reduce bank-level conflicts and increase the bandwidth on a field-programmable gate array. In this work, we propose a memory partitioning approach for multi-pattern data access. First, we propose to combine multiple patterns into a single pattern to reduce the complexity of multi-pattern. Then, we propose to perform data reuse analysis on the combined pattern to find data reuse opportunities and the non-reusable data pattern. Finally, an efficient bank mapping algorithm with low complexity and low overhead is proposed to find the optimal memory partitioning solution. Experimental results demonstrated that compared to the state-of-the-art method, our proposed approach can reduce the number of block RAMS by 58.9% on average, with 79.6% reduction in SLICEs, 85.3% reduction in LUTs, 67.9% in reduction Flip-Flops, 54.6% reduction in DSP48Es, 83.9% reduction in SRLs, 50.0% reduction in storage overhead, 95.0% reduction in execution time, and 77.3% reduction in dynamic power consumption on average. Meanwhile, the performance can be improved by 14.0% on average.
Exploring Hemodynamic Responses Using Mirror Visual Feedback With Electromyogram-Triggered Stimulation and Functional Near-Infrared Spectroscopy

In recent years, mirror visual feedback (MVF) therapy combined with electrical stimulation (ES) have been proposed for patients with hemiparesis. However, the neurophysiological effect remains unknown. We investigated the effects of MVF by itself and along with electromyogram-triggered ES (ETES) on hemodynamic responses using functional near-infrared spectroscopy (NIRS). Eighteen healthy subjects participated in this study. We measured changes in brain oxygenation using 48 NIRS channels. We investigated the effects of three main factors of visual feedback (observation of a mark, right hand, and hand movements via mirror) with or without ES on bilateral precentral gyrus (PrG), postcentral gyrus (PoG), supplementary motor area (SMA), supramarginal gyrus area (SMG), and angular gyrus (AG) to determine the contribution of each factor. The results showed that the left PoG was significantly more activated when performing mirrored tasks (MT) than when performing circle or Right-hand Tasks (RTs). In addition, the right PoG and right SMA in MT were significantly more activated than in MT + ES cases. Our findings suggested that observation of movements through the mirror caused activation of the postcentral gyrus rather than the PrG, and MVF along with ETES decreased cortical activation.
Olympus: Sensor Privacy through Utility Aware Obfuscation

Abstract Personal data garnered from various sensors are often offloaded by applications to the cloud for analytics. This leads to a potential risk of disclosing private user information. We observe that the analytics run on the cloud are often limited to a machine learning model such as predicting a user’s activity using an activity classifier. We present Olympus, a privacy framework that limits the risk of disclosing private user information by obfuscating sensor data while minimally affecting the functionality the data are intended for. Olympus achieves privacy by designing a utility aware obfuscation mechanism, where privacy and utility requirements are modeled as adversarial networks. By rigorous and comprehensive evaluation on a real world app and on benchmark datasets, we show that Olympus successfully limits the disclosure of private information without significantly affecting functionality of the application.
Impaired Contracture of 3D Collagen Constructs by Fibronectin-Deficient Murine Fibroblasts

Fibronectin (FN) is an extracellular matrix glycoprotein that is abundantly expressed by fibroblasts in contracting wounds, where it mediates cell adhesion, migration and proliferation. FN also efficiently binds to collagen. Therefore, we and others hypothesized that FN and its cellular receptor integrin α5β1 might be involved in collagen matrix contracture by acting as linkers. However, there are conflicting reports on this issue. Moreover, several publications suggest an important role of collagen-binding integrin receptors α2β1 and α11β1 in collagen matrix contracture. Therefore, the aim of the present study was to determine the contributions of FN–integrin α5β1 interactions relative to those of collagen receptors α2β1 and α11β1 in this process. To assess the role of cellular FN directly, we employed FN-deficient mouse fibroblasts, subjected them to a collagen gel contracture assay in vitro, and compared them to their wildtype counterparts. Exogenous FN was removed from serum-containing medium. For dissecting the role of major collagen receptors, we used two FN-deficient mouse fibroblast lines that both possess integrin α5β1 but differ in their collagen-binding integrins. Embryo-derived FN-null fibroblasts, which express α11- but no α2-integrin, barely spread and tended to cluster on collagen gels. Moreover, FN-null fibroblasts required exogenously added FN to assemble α5β1-integrin in fibrillar adhesion contacts, and to contract collagen matrices. In contrast, postnatal kidney fibroblasts were found to express α2- but barely α11-integrin. When FN expression was suppressed in these cells by shRNA transfection, they were able to spread on and partially contract collagen gels in the absence of exogenous FN. Also in this case, however, collagen contracture was stimulated by adding FN to the medium. Antibody to integrin α5β1 or RGD peptide completely abolished collagen contracture by FN-deficient fibroblasts stimulated by FN addition. We conclude that although collagen-binding integrins (especially α2β1) can mediate contracture of fibrillar collagen gels by murine fibroblasts to some extent, full activity is causally linked to the presence of pericellular FN and its receptor integrin α5β1.
Enhanced Global-Brain Functional Connectivity in the Left Superior Frontal Gyrus as a Possible Endophenotype for Schizophrenia

The notion of dysconnectivity in schizophrenia has been put forward for many years and results in substantial attempts to explore altered functional connectivity (FC) within different networks with inconsistent results. Clinical, demographical, and methodological heterogeneity may contribute to the inconsistency. Forty-four patients with first-episode, drug-naive schizophrenia, 42 unaffected siblings of schizophrenia patients and 44 healthy controls took part in this study. Global-brain FC (GFC) was employed to analyze the imaging data. Compared with healthy controls, patients with schizophrenia and unaffected siblings shared enhanced GFC in the left superior frontal gyrus (SFG). In addition, patients had increased GFC mainly in the thalamo-cortical network, including the bilateral thalamus, bilateral posterior cingulate cortex (PCC)/precuneus, left superior medial prefrontal cortex (MPFC), right angular gyrus, and right SFG/middle frontal gyrus and decreased GFC in the left ITG/cerebellum Crus I. No other altered GFC values were observed in the siblings group relative to the control group. Further ROC analysis showed that increased GFC in the left SFG could separate the patients or the siblings from the controls with acceptable sensitivities. Our findings suggest that increased GFC in the left SFG may serve as a potential endophenotype for schizophrenia.
High Cortisol and the Risk of Dementia and Alzheimer’s Disease: A Review of the Literature

Introduction: Cortisol effects on the brain are exerted through two distinct receptors, inducing complex and even opposite effects on the cerebral structures implicated in the various cognitive functions. High cortisol may also have deleterious effects on the brain structures and contribute to neurodegeneration, in particular Alzheimer’s disease (AD), via different mechanisms. Objective: To examine the interrelationships between cortisol, cognitive impairment and AD. Methods: Review of the literature. Results: Clinical studies found that elevated cortisol was associated with poorer overall cognitive functioning, as well as with poorer episodic memory, executive functioning, language, spatial memory, processing speed, and social cognition; while in animals, glucocorticoid administration resulted in cognitive impairment and abnormal behavior. In cognitively healthy subjects, higher cortisol levels have been associated with an increased risk of cognitive decline and AD. Subjects with dementia and Mild Cognitive Impairment (MCI) due to AD have been found to have higher CSF cortisol levels than cognitively healthy controls. Elevated CSF cortisol may also be associated with a more rapid cognitive decline in MCI due to AD. Elevated cortisol levels have been also found in delirium. High cortisol may mediate the impact of stressful life events, high neuroticism, depression, sleep disturbances, as well as cardiovascular risk factors on cognitive performance, neurodegeneration, and cognitive decline. High cortisol may also exert neurotoxic effects on the hippocampus, and promote oxidative stress and amyloid β peptide toxicity. Further possible underlying mechanisms include the interactions of cortisol with inflammatory mediators, neurotransmitters, and growth factors. Conclusion: Elevated cortisol levels may exert detrimental effects on cognition and contribute to AD pathology. Further studies are needed to investigate cortisol-reducing and glucocorticoidreceptor modulating interventions to prevent cognitive decline.
Melt Procedure Affects the Photosynthetic Response of Sea Ice Algae

The accuracy of sea ice algal production estimates is influenced by the range of melting procedures used in studies to obtain a liquid sample for incubation, particularly in relation to the duration of melt and the approach to buffering for osmotic shock. In this research, ice algal photophysiology from 14C incubations was compared in field samples prepared by three melt procedures: i) a rapid ≤ 4 h melt of the bottommost (< 1 cm) ice algal layer scraped into a large volume of filtered seawater (salinity 27 - 30), ii) melt of a bottom 5 cm section diluted into a moderate volume of filtered seawater over 24 h (salinity 20 - 24), and iii) melt of a bottom 5 cm section without any filtered seawater dilution over about 48 h (salinity 10 -12). Maximum photosynthetic rate, photosynthetic efficiency and production at zero irradiance were significantly affected by the melt treatment employed in experiments. All variables were greatest in the highly diluted scrape sample and lowest in the bulk-ice samples melted in the absence of filtered seawater. Laboratory experiments exposing cultures of the common sea ice diatom Nitzschia frigida to different salinities and light conditions suggested that the field-based responses can be attributed to the rapid (< 4 h) adverse effects of exposing cells to low salinities during melt without dilution. The observed differences in primary production between melt treatments were estimated to account for over 60% of the variability in production estimates reported for the Arctic. Future studies are strongly encouraged to replicate salinity conditions representative of in situ values during the melting process to minimize hypoosmotic stress, thereby most accurately estimating primary production.
Plant-Derived Polyphenols Modulate Human Dendritic Cell Metabolism and Immune Function via AMPK-Dependent Induction of Heme Oxygenase-1

Polyphenols are important immunonutrients which have been investigated in the context of inflammatory and autoimmune disease due to their significant immunosuppressive properties. However, the mechanism of action of many polyphenols is unclear, particularly in human immune cells. The emerging field of immunometabolism has highlighted the significance of metabolic function in the regulation of immune cell activity, yet the effects of polyphenols on immune cell metabolic signaling and function has not been explored. We have investigated the effects of two plant-derived polyphenols, carnosol and curcumin, on the metabolism of primary human dendritic cells (DC). We report that human DC display an increase in glycolysis and spare respiratory capacity in response to LPS stimulation, which was attenuated by both carnosol and curcumin treatment. The regulation of DC metabolism by these polyphenols appeared to be mediated by their activation of the cellular energy sensor, AMP-activated Protein Kinase (AMPK), which resulted in the inhibition of mTOR signaling in LPS-stimulated DC. Previously we have reported that both carnosol and curcumin can regulate the maturation and function of human DC through upregulation of the immunomodulatory enzyme, Heme Oxygenase-1 (HO-1). Here we also demonstrate that the induction of HO-1 by polyphenols in human DC is dependent on their activation of AMPK. Moreover, pharmacological inhibition of AMPK was found to reverse the observed reduction of DC maturation by carnosol and curcumin. This study therefore describes a novel relationship between metabolic signaling via AMPK and HO-1 induction by carnosol and curcumin in human DC, and characterizes the effects of these polyphenols on DC immunometabolism for the first time. These results expand our understanding of the mechanism of action of carnosol and curcumin in human immune cells, and suggest that polyphenol supplementation may be useful to regulate the metabolism and function of immune cells in inflammatory and metabolic disease.
A 32-Gb/s PAM-4 Quarter-Rate Clock and Data Recovery Circuit With an Input Slew-Rate Tolerant Selective Transition Detector

We present a 32-Gb/s PAM-4 quarter-rate clock and data recovery (CDR) circuit having a newly proposed selective transition detector (STD). The STD allows phase detection of PAM-4 data in a simple manner by eliminating middle transition and majority voting with simple logic gates. In addition, using the edge-rotating technique with quarter-rate CDR operation, our CDR achieves power consumption and chip area reduction. A prototype 32-Gb/s quarter-rate PAM-4 CDR circuit is realized with 28-nm CMOS technology. The CDR circuit consumes 32 mW with 1.2-V supply and the recovered clock signal has 0.0136-UI rms jitter.