Miracle-dz/UniFAR-FTUs huggingface dataset:
Context-aware Adaptive Surgery

Deep Neural Networks (DNNs) have made massive progress in many fields and deploying DNNs on end devices has become an emerging trend to make intelligence closer to users. However, it is challenging to deploy large-scale and computation-intensive DNNs on resource-constrained end devices due to their small size and lightweight. To this end, model partition, which aims to partition DNNs into multiple parts to realize the collaborative computing of multiple devices, has received extensive research attention. To find the optimal partition, most existing approaches need to run from scratch under given resource constraints. However, they ignore that resources of devices (e.g., storage, battery power), and performance requirements (e.g., inference latency), are often continuously changing, making the optimal partition solution change constantly during processing. Therefore, it is very important to reduce the tuning latency of model partition to realize the real-time adaption under the changing processing context. To address these problems, we propose the Context-aware Adaptive Surgery (CAS) framework to actively perceive the changing processing context, and adaptively find the appropriate partition solution in real-time. Specifically, we construct the partition state graph to comprehensively model different partition solutions of DNNs by import context resources. Then "the neighbor effect" is proposed, which provides the heuristic rule for the search process. When the processing context changes, CAS adopts the runtime search algorithm, Graph-based Adaptive DNN Surgery (GADS), to quickly find the appropriate partition that satisfies resource constraints under the guidance of the neighbor effect. The experimental results show that CAS realizes adaptively rapid tuning of the model partition solutions in 10ms scale even for large DNNs (2.25x to 221.7x search time improvement than the state-of-the-art researches), and the total inference latency still keeps the same level with baselines.
The Antimicrobial Peptide MK58911-NH2 Acts on Planktonic, Biofilm, and Intramacrophage Cells of Cryptococcus neoformans

Cryptococcosis is associated with high rates of morbidity and mortality, especially in AIDS patients. Its treatment is carried out by combining amphotericin B and azoles or flucytosine, which causes unavoidable toxicity issues in the host. ABSTRACT Cryptococcosis is associated with high rates of morbidity and mortality, especially in AIDS patients. Its treatment is carried out by combining amphotericin B and azoles or flucytosine, which causes unavoidable toxicity issues in the host. Thus, the urgency in obtaining new antifungals drives the search for antimicrobial peptides (AMPs). This study aimed to extend the understanding of the mechanism of action of an AMP analog from wasp peptide toxins, MK58911-NH2, on Cryptococcus neoformans. We also evaluated if MK58911-NH2 can act on cryptococcal cells in macrophages, biofilms, and an immersion zebrafish model of infection. Finally, we investigated the structure-antifungal action and the toxicity relationship of MK58911-NH2 fragments and a derivative of this peptide (MH58911-NH2). The results demonstrated that MK58911-NH2 did not alter the fluorescence intensity of the cell wall-binding dye calcofluor white or the capsule-binding dye 18b7 antibody-fluorescein isothiocyanate (FITC) in C. neoformans but rather reduced the number and size of fungal cells. This activity reduced the fungal burden of C. neoformans in both macrophages and zebrafish embryos as well as within biofilms. Three fragments of the MK58911-NH2 peptide showed no activity against Cryptococcus and not toxicity in lung cells. The derivative peptide MH58911-NH2, in which the lysine residues of MK58911-NH2 were replaced by histidines, reduced the activity against extracellular and intracellular C. neoformans. On the other hand, it was active against biofilms and showed reduced toxicity. In summary, these results showed that peptide MK58911-NH2 could be a promising agent against cryptococcosis. This work also opens a perspective for the verification of the antifungal activity of other derivatives.
Mapping quantitative trait loci for drought tolerance/susceptibility indices and estimation of breeding values of doubled haploid lines in wheat (Triticum aestivum)

Abstract. Water shortage and drought stress in the reproductive stage of wheat (Triticum aestivum L.) considerably affect grain yield (GY). Mapping genes for drought tolerance assists in selection for drought improvement. In the present study, we evaluated breeding values based on best linear unbiased predictions (BLUPs) and drought tolerance/susceptibility indices (DT/SIs), and identified marker–phenotype associations in 220 doubled haploid (DH) lines. The DH lines were evaluated for GY and 1000-grain weight (TGW) under drought stress and well-watered conditions at the heading stage in 2015 and 2016. The linkage map comprised 1333 SSR, DArT and SNP markers with an average density of 2.18 markers per cM. The BLUPs were significantly correlated with GY of the lines. Significant correlations were found between stress tolerance score (STS) and drought response index, yield index, yield stability index, geometric mean productivity and stress tolerance index. The lines DH_R295 and DH_R360 had the highest breeding values for GY and STS. Major QTLs, one main effect and eight epistatic, were identified for the DT/SIs. A major QTL was identified for STS-GY, which explained 11.39% of the STS-GY variation in 2015. This QTL was co-located with QTLs for yield index-GY and yield stability index-GY within the BS00066932_51–gwm0314b marker interval (48 cM on 3B). The search for gene annotation showed that BS00066932_51 overlapped with protein-encoding genes. In conclusion, the QTL-linked markers help genotype selection for the improvement of drought tolerance, and they are good candidates for use in genomic selection.
Isoform-Specific Reduction of the Basic Helix-Loop-Helix Transcription Factor TCF4 Levels in Huntington’s Disease

Abstract Huntington’s disease (HD) is an inherited neurodegenerative disorder with onset of characteristic motor symptoms at midlife, preceded by subtle cognitive and behavioral disturbances. Transcriptional dysregulation emerges early in the disease course and is considered central to HD pathogenesis. Using wild-type (wt) and HD knock-in mouse striatal cell lines we observed a HD genotype-dependent reduction in the protein levels of transcription factor 4 (TCF4), a member of the basic helix-loop-helix (bHLH) family with critical roles in brain development and function. We characterized mouse Tcf4 gene structure and expression of alternative mRNAs and protein isoforms in cell-based models of HD, and in four different brain regions of male transgenic HD mice (R6/1) from young to mature adulthood. The largest decrease in the levels of TCF4 at mRNA and specific protein isoforms were detected in the R6/1 mouse hippocampus. Translating this finding to human disease, we found reduced expression of long TCF4 isoforms in the postmortem hippocampal CA1 area and in the cerebral cortex of HD patients. Additionally, TCF4 protein isoforms showed differential synergism with the proneural transcription factor ASCL1 in activating reporter gene transcription in hippocampal and cortical cultured neurons. Induction of neuronal activity increased these synergistic effects in hippocampal but not in cortical neurons, suggesting brain region-dependent differences in TCF4 functions. Collectively, this study demonstrates isoform-specific changes in TCF4 expression in HD that could contribute to the progressive impairment of transcriptional regulation and neuronal function in this disease.
Physicochemical and sensory properties of pawpaw ( Carica papaya Linn) flavoured yoghurt

Flavoured yoghurts are widely produced by using synthetic flavourings in Cameroon. However, the addition of fruits to yoghurt will impart natural flavours as well as contribute to the welfare of consumers by enhancing the nutritive and the functional properties of the yoghurt. This study was, therefore, aimed at evaluating the physicochemical and sensory properties of pawpaw ( Carica papaya L.) flavoured yoghurt. Yoghurt was produced with the incorporation of pawpaw puree at four levels: 0% (P 0 as control), 5% (P 1 ), 10% (P 2 ) and 15% (P 3 ). The yoghurt samples were submitted to some physicochemical analysis (pH, titratable acidity, dry matter, moisture content, fat content, Solid-Non-Fat (SNF), sugar content and viscosity) on days 0, 7, 14, and 21 of storage. The sensory characteristics assessed by an untrained panel of 30 members were: flavour, colour, taste and texture. The pH of P 0 (5.01±0.04) and P 3 (4.99±0.04) and also the fat content of P 0 (3.4±0.17%) were significantly (P≤0.05) higher compared to other samples. There was a reduction of fat content in yoghurt with an increase of pawpaw puree. Sugar content, SNF and viscosity of yoghurt increased significantly (P≤0.05) with addition of pawpaw puree. Meanwhile, dry matter and titratable acidity were not significantly (P≥0.05) affected. The titratable acidity of yoghurt P 0 and P 3 significantly (P≤0.05) increased up to day seven of storage while pH was decreasing. From days 14 to 21, yoghurt P 2 and yoghurts P 2 and P 3 did not present significant (P≥0.05) decrease of titratable acidity and pH, respectively. The fat content of P 0 and P1, reduced significantly (P≤0.05) the first week and the second weeks of storage, respectively, and then remained comparable (P≥0.05) to the end of the storage period. There was no significant (P≥0.05) difference in sensory properties of all the yoghurt treatments. In conclusion, the use of pawpaw to flavour yoghurt did not negatively affect the yoghurt properties; therefore, pawpaw flavoured yoghurt can be recommended for consumption. Keys words : Flavoured yoghurt, pawpaw puree, physicochemical properties, storage, sensory properties
Data Mountain: Self-Monitoring, Goal Setting, and Positive Attributions to Enhance the Oral Reading Fluency of Elementary Students With or at Risk for Reading Disabilities

Data Mountain is a self-determination program that has shown early promise in enhancing the oral reading fluency (ORF) of students with or at risk for reading disabilities (RD). This program supports self-determined learning behaviors through explicit teaching of self-monitoring, goal setting, and positive attributions. The present study tested the effects of Data Mountain on the ORF of 81 students with or at risk for RD in second through fifth grades, randomly assigned to one of three conditions: Data Mountain delivered in small groups, Data Mountain delivered individually, or a comparison condition. Results from hierarchical linear modeling indicated that treatment students read an average of 31 more words per minute with a growth rate twice that of comparison students (p < .01). The transferable possibilities of Data Mountain to provide students with an opportunity to learn self-determination skills and support ORF is significant to the field of special education.
Do peripheral protein oligomers in neurodegenerative diseases shape T cell responses beyond the brain?

Neurodegenerative diseases place a devastating burden on affected individuals and their families, and new treatments are desperately needed for these common immune‐mediated inflammatory conditions. While large aggregates of abnormal proteins in the brain cause significant damage, it is becoming clear that smaller soluble protein aggregates can also contribute to disease, by both direct and indirect mechanisms. These soluble protein oligomers can be found in patients' serum. Here, we describe recent research that identifies effects of model oligomer molecules on peripheral blood T cells, therefore providing an additional mechanism by which neurodegeneration may be worsened through amplification of peripheral adaptive immune responses.
Transferrin receptor 1-mediated iron uptake regulates bone mass in mice via osteoclast mitochondria and cytoskeleton

Increased intracellular iron spurs mitochondrial biogenesis and respiration to satisfy high-energy demand during osteoclast differentiation and bone-resorbing activities. Transferrin receptor 1 (TFR1) mediates cellular iron uptake through endocytosis of iron-loaded transferrin and its expression increases during osteoclast differentiation. Nonetheless, the precise functions of TFR1 and TFR1-mediated iron uptake in osteoclast biology and skeletal homeostasis remain incompletely understood. To investigate the role of TFR1 in osteoclast lineage cells, we conditionally deleted Tfr1 gene in myeloid precursors or mature osteoclasts by crossing Tfr1- floxed mice with LysM-Cre and Ctsk-Cre mice, respectively. Skeletal phenotyping by µCT and histology unveiled that loss of Tfr1 in osteoclast progenitor cells resulted in a three-fold increase in trabecular bone mass in the long bones of 10-week old female but not male mice. Although high trabecular bone volume in long bones was seen in both male and female mice with deletion of Tfr1 in mature osteoclasts, this phenotype was more pronounced in female knockout mice. Mechanistically, disruption of Tfr1 expression attenuated mitochondrial metabolism and cytoskeletal organization in mature osteoclasts, leading to decreased bone resorption with no impact on osteoclastogenesis. These results indicate that Tfr1-mediated iron uptake is specifically required for osteoclast function and is indispensable for bone remodeling.
STK25 and MST3 Have Overlapping Roles to Regulate Rho GTPases during Cortical Development

Precise control of neuronal migration is required for the laminar organization of the neocortex and critical for brain function. We previously reported that the acute disruption of the Stk25 gene (Stk25 conditional knock-out; cKO) during mouse embryogenesis causes anomalous neuronal migration in the neocortex, but paradoxically the Stk25 cKO did not have a cortical phenotype, suggesting some forms of compensation exist. In this study, we report that MST3, another member of the GCKIII subgroup of the Ste20-like kinase family, compensates for loss of Stk25 and vice versa with sex independent manner. MST3 overexpression rescued neuronal migration deficit and abnormal axonogenesis in Stk25 cKO brains. Mechanistically, STK25 leads to Rac1 activation and reduced RhoA levels in the developing brain, both of which are required to fully restore neuronal migration in the Stk25 cKO brain. Abnormal migration phenotypes are also rescued by overexpression of Bacurd1and Cul3, which target RhoA for degradation, and activate Rac1. This study reveals that MST3 upregulation is capable of rescuing acute Stk25 deficiency and resolves details of signaling downstream STK25 required for corticogenesis both common to and distinct from MST3 signaling. SIGNIFICANCE STATEMENT Proper neuronal migration during cortical development is required for normal neuronal function. Here, we show that STK25 and MST3 kinases regulate neuronal migration and polarization in a mutually compensatory manner. Furthermore, STK25 balances Rac1 activity and RhoA level through forming complexes with α-PIX and β-PIX, GTPase regulatory enzymes, and Cullin3-Bacurd1/Kctd13, a pair of RhoA ubiquitination molecules in a kinase activity-independent manner. Our findings demonstrate the importance of overlapping and unique roles of STK25 and MST3 to regulate Rho GTPase activities in cortical development.
Generic and Specific Cell Adhesion

The development of a technique to measure the adhesion forces of receptor-ligand pairs under biocompatible conditions is the main focus of this thesis. The established reflection-interference contrast microscopy technique is upgraded to allow for measurements of the absolute distances between adhering membranes and solid surfaces. Giant vesicles are used to study the receptor-mediated adhesion to solid supported membranes. Introducing a soft polymer film between substrate and membrane makes it possible to attach receptors to surfaces without a considerable loss of their functionality. Absolute unbinding forces can be determined by the controlled detachment of the adhered giant vesicles from the substrate using magnetic tweezers. Moreover, the generic unbinding is shown to be a first order phase transition from an detailed analysis of the membrane fluctuations.
Long-Term Predictions of Bike-Sharing Stations? Bikes Availability

Bike-sharing systems are present in many cities as a valid alternative to fuel-based public transports since they are eco-friendly, prevent traffic congestions, reduce the probability of social contacts. On the other hand, bike-sharing present some problems such as the irregular distribution of bikes on the stations/racks/areas (still very used for e-bikes) and for the final users the difficulty of knowing in advance their status with a certain degree of confidence, whether there will be available bikes at a specific bike-station at a certain time of the day, or a free slot for leaving the rented bike. Therefore, providing predictions can be useful for improving the quality of e-bike services. This paper presents a technique to predict the number of available bikes and free bike slots in bike-sharing stations (the best solution for e-bikes). To this end, a set of features and predictive models have been developed and compared to identify the best prediction model for long-term predictions (24 hours in advance). The solution and its validation have been performed by using data collected in bike stations in the cities of Siena and Pisa, in the context of Sii-Mobility National Research Project on Mobility and Transport and Snap4City Smart City IoT infrastructure. The Random Forest (RF) and Gradient Boosting Machine (GBM) offer a robust approach for the implementation of reliable and fast predictions of available bikes in terms of flexibility and robustness to critical cases, producing longterms predictions in critical conditions (i.e., when there are only few remaining available bikes on the
A Counter-Extrapolation Approach for the Boundary Velocity Calculation in Immersed Boundary Simulations

The immersed boundary method (IBM) is often adopted to simulate various flow systems. The two key steps in IBM, namely the force distribution and velocity interpolation steps, are both performed in the immersed boundary layer region. As a result, the flow velocity in this area becomes less reliable, and the boundary velocity calculated from the local flow is less accurate. To enhance the boundary velocity accuracy, here we propose the counter-extrapolation method (CEM), which estimates the boundary velocity using the flow velocity outside of the immersed boundary layer, and thus effectively improved the accuracy in the calculated velocity. Several benchmark tests, which involve flat and curved boundaries and steady and unsteady flows, are conducted; and CEM is compared to other IBM variants recently proposed in the literature. Our results show remarkable accuracy improvements in flow velocity and flow-structure interaction from CEM compared to other methods.
Chasing the Tail of Cosmic Reionization with Dark Gap Statistics in the Lyα Forest over 5 < z < 6

We present a new investigation of the intergalactic medium (IGM) near the end of reionization using “dark gaps” in the Lyα forest. Using spectra of 55 QSOs at z em > 5.5, including new data from the XQR-30 VLT Large Programme, we identify gaps in the Lyα forest where the transmission averaged over 1 comoving h −1 Mpc bins falls below 5%. Nine ultralong (L > 80 h −1 Mpc) dark gaps are identified at z < 6. In addition, we quantify the fraction of QSO spectra exhibiting gaps longer than 30 h −1 Mpc, F 30, as a function of redshift. We measure F 30 ≃ 0.9, 0.6, and 0.15 at z = 6.0, 5.8, and 5.6, respectively, with the last of these long dark gaps persisting down to z ≃5.3. Comparing our results with predictions from hydrodynamical simulations, we find that the data are consistent with models wherein reionization extends significantly below redshift six. Models wherein the IGM is essentially fully reionized that retain large-scale fluctuations in the ionizing UV background at z ≲6 are also potentially consistent with the data. Overall, our results suggest that signatures of reionization in the form of islands of neutral hydrogen and/or large-scale fluctuations in the ionizing background remain present in the IGM until at least z ≃ 5.3.
The microRNA-451a/chromosome segregation 1-like axis suppresses cell proliferation, migration, and invasion and induces apoptosis in nasopharyngeal carcinoma

ABSTRACT MicroRNA-451a (miR-451a) has been implicated in the initiation and progression of multiple cancers. However, the regulatory mechanisms underlying its function in nasopharyngeal carcinoma (NPC) are poorly understood. Thus, we investigated in detail the role of the microRNA-451a/chromosome segregation 1-like (miR-45a/CSE1L) axis and its regulatory mechanism in NPC. We examined the levels of miR-451a and CSE1L in NPC, and assessed the effects of miR-451a and CSE1L on NPC by cell functional experiments. Furthermore, we elucidated the direct regulatory effect of miR-451a on CSE1L by the luciferase reporter assay, RNA pull-down assay, and RNA immunoprecipitation and validated our observations by calculating the Pearson’s correlation coefficient. We found that miR-451a was down-regulated in NPC cells, and its over-expression attenuated cell proliferation, migration, and invasion, and tumor growth in 5–8 F and SUNE-1 cells and promoted apoptosis. Moreover, CSE1L was the direct gene target of miR-451a, and its over-expression abrogated miR-451a-dependent inhibition of malignancy in 5–8 F and SUNE-1 cells. The Pearson’s correlation coefficient indicated a negative correlation between CSE1L and miR-451a. miR-451a serves as a tumor suppressor and targets CSE1L. miR-451a suppresses CSE1L expression, thereby reducing proliferation, invasion, and migration and increasing apoptosis of NPC cells.
Smartphone-Based Tapping Frequency as a Surrogate for Perceived Fatigue

Fatigue is a common symptom in various diseases, including multiple sclerosis (MS). The current standard method to assess fatigue is through questionnaires, which has several shortcomings; questionnaires are subjective, prone to recall bias, and potentially confounded by other symptoms like stress and depression. Thus, there is an unmet medical need to develop objective and reliable methods to evaluate fatigue. Our study seeks to develop an objective and ubiquitous monitoring tool for assessing fatigue. Leveraging a smartphone-based rapid tapping task, we conducted a two-week in-the-wild study with 35 MS patients. We explore the association between tapping derived metrics and perceived fatigue assessed with two standard clinical scales: fatigue severity scale (FSS) and fatigue scale for motor and cognitive function (FSMC). Our novel smartphone-based fatigue metric, mean tapping frequency, objectively ranks perceived fatigue with a mean AUCROC = . 76, CI = [. 71, . 81] according to the FSMC, and a mean AUCROC = . 81, CI = [. 76, . 86] according to the FSS. These results demonstrate that our approach is feasible and valid in uncontrolled environments. In this work, we provide a promising tool for objective fatigue monitoring to be used in clinical trials and routine medical care.