Miracle-dz/UniFAR-FTUs huggingface dataset:
Examining Online Practices of an Autism Parent Community in Turkey: Goals, Needs, and Opportunities

Autism is a complex, life-long condition that manifests itself in unique ways in each person. Due to the complexity of the condition along with not having efficient and immediate social support, parents with autistic children often seek for and rely upon the information generated by the community (parents, caregivers, autistics and experts) on online platforms. We look into what parents of autistic individuals discuss on an online platform in Turkey, how they practice autism online and why those practices are important or relevant. Our findings show how parents cope with understanding and defining autism, and how they seek for empowering each other, and managing the everyday collectively under a dominant medical discourse around autism in Turkish context. Based on our findings, we extend the existing knowledge on collective and alternative ways of re-defining autism as lived experience and introduce recommendations on how those strategies can be integrated to design.
Circus, Play and Technology Probes: Training Body Awareness and Control with Children

Physical training can be frustrating and hard, especially for those who experience additional challenges to access and control their proprioceptive senses. In the context of designing for children with Sensory-based Motor Disorder, we designed and deployed a series of Training Technology Probes to be used in circus training. Here we focus on how these were used, tested, and appropriated by children and instructors during a six-week circus training course. Through these explorations, we identified a range of potential benefits from using their functions in training. We present the Physical Training Technology Probes and the benefits they brought to training. We show how the technology functions helped children focus and provided feedback related to posture and balance. Furthermore, their open-ended designs and versatile options for use were crucial in exploring their contributions to training, and in how they helped foster creative engagement with technology and training. Our work contributes towards understanding the specific requirements when designing for the target group, and more generally contributes with design strategies for technology support for skill training.
Modus Operandi: The Implications from Redesigning Moded Experiments in Multitouch User Interfaces

Evaluation of moded interaction techniques is essential in determining the optimal strategy to switch between the modes of a user interface. Performance can be evaluated when each technique is used to complete a given set of changing mode sequences. However, there have been limited variations in the patterns adopted by past studies, because all of their mode sequences were consistently presented in chunks of only 5 tasks at a time. Our study addresses the identified gap by expanding the chunk size by at least 10 times and diversifying the independent variables (i.e. patterns). Although we found that Persist outperforms User-Maintained Interaction technique overall, patterns with a clear presence of dominating mode are ideal for the latter (and supported locking feature) to thrive. Our findings show how an experimental modification can augment the existing understanding of moded interaction.
Data Platform for Machine Learning

In this paper, we present a purpose-built data management system, MLdp, for all machine learning (ML) datasets. ML applications pose some unique requirements different from common conventional data processing applications, including but not limited to: data lineage and provenance tracking, rich data semantics and formats, integration with diverse ML frameworks and access patterns, trial-and-error driven data exploration and evolution, rapid experimentation, reproducibility of the model training, strict compliance and privacy regulations, etc. Current ML systems/services, often named MLaaS, to-date focus on the ML algorithms, and offer no integrated data management system. Instead, they require users to bring their own data and to manage their own data on either blob storage or on file systems. The burdens of data management tasks, such as versioning and access control, fall onto the users, and not all compliance features, such as terms of use, privacy measures, and auditing, are available. MLdp offers a minimalist and flexible data model for all varieties of data, strong version management to guarantee re-producibility of ML experiments, and integration with major ML frameworks. MLdp also maintains the data provenance to help users track lineage and dependencies among data versions and models in their ML pipelines. In addition to table-stake features, such as security, availability and scalability, MLdp's internal design choices are strongly influenced by the goal to support rapid ML experiment iterations, which cycle through data discovery, data exploration, feature engineering, model training, model evaluation, and back to data discovery. The contributions of this paper are: 1) to recognize the needs and to call out the requirements of an ML data platform, 2) to share our experiences in building MLdp by adopting existing database technologies to the new problem as well as by devising new solutions, and 3) to call for actions from our communities on future challenges.
Top-k Queries over Digital Traces

Recent advances in social and mobile technology have enabled an abundance of digital traces (in the form of mobile check-ins, association of mobile devices to specific WiFi hotspots, etc.) revealing the physical presence history of diverse sets of entities (e.g., humans, devices, and vehicles). One challenging yet important task is to identify k entities that are most closely associated with a given query entity based on their digital traces. We propose a suite of indexing techniques and algorithms to enable fast query processing for this problem at scale. We first define a generic family of functions measuring the association between entities, and then propose algorithms to transform digital traces into a lower-dimensional space for more efficient computation. We subsequently design a hierarchical indexing structure to organize entities in a way that closely associated entities tend to appear together. We then develop algorithms to process top-k queries utilizing the index. We theoretically analyze the pruning effectiveness of the proposed methods based on a mobility model which we propose and validate in real life situations. Finally, we conduct extensive experiments on both synthetic and real datasets at scale, evaluating the performance of our techniques both analytically and experimentally, confirming the effectiveness and superiority of our approach over other applicable approaches across a variety of parameter settings and datasets.
Safety of combined salivary gland and multilevel intramuscular onabotulinumtoxinA injections with and without ethanol in pediatric patients with cerebral palsy: A retrospective study.

OBJECTIVE To evaluate the safety of combining salivary gland onabotulinumtoxinA (BTX-A) injections for sialorrhea with intramuscular BTX-A injections for spasticity in the same procedure. DESIGN A retrospective cohort study in a tertiary hospital center. Patients selected were younger than 20 years, diagnosed with cerebral palsy, and received their first salivary gland BTX-A injection between March 2011 and July 2015. Chart reviews and telephone interviews were performed. The primary outcome measure was the rate of adverse events after combined BTX-A injections into salivary glands and muscles. The secondary outcome measure was the efficacy of injections, as reported by patients. RESULTS Twenty-five of the 52 selected patients received salivary gland BTX-A injections only, and 27 received concurrent salivary gland and multi-level intramuscular chemodenervation with BTX-A injections. The rate of adverse events was < 10% in both groups: 4% in "salivary only" group and 7% in the group with salivary + multi-level intramuscular chemodenervation with BTX-A (with or without alcohol). Both approaches were equally effective in meeting their goals of salivary injections (> 50% improvement for at least two months). In the "salivary only" and in the "salivary + multi-level intramuscular" group, 76 and 85% of the patients reached their goals respectively. CONCLUSIONS Combining BTX-A injections for sialorrhea with multilevel intramuscular BTX-A injections (with or without alcohol) appears to be safe and effective and allows treatment of patients for both conditions simultaneously.
Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157

Intensive surveillance for enterohemorrhagic Escherichia coli (EHEC) serogroup O157 is important to detect outbreaks and to prevent the spread of the bacterium. Recent advances in sequencing technology made molecular surveillance using whole-genome sequence (WGS) realistic. To develop rapid, high-throughput, and cost-effective typing methods for real-time surveillance, typing resolution of WGS and a conventional typing method, multilocus variable-number tandem-repeat analysis (MLVA), was evaluated. Nation-level systematic comparison of MLVA, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) indicated that a combination of WGS and MLVA is a realistic approach to improve EHEC O157 surveillance. ABSTRACT Due to the potential of enterohemorrhagic Escherichia coli (EHEC) serogroup O157 to cause large food borne outbreaks, national and international surveillance is necessary. For developing an effective method of molecular surveillance, a conventional method, multilocus variable-number tandem-repeat analysis (MLVA), and whole-genome sequencing (WGS) analysis were compared. WGS of 369 isolates of EHEC O157 belonging to 7 major MLVA types and their relatives were subjected to comprehensive in silico typing, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) analyses. The typing resolution was the highest in cgSNP analysis. However, determination of the sequence of the mismatch repair protein gene mutS is necessary because spontaneous deletion of the gene could lead to a hypermutator phenotype. MLVA had sufficient typing resolution for a short-term outbreak investigation and had advantages in rapidity and high throughput. cgMLST showed less typing resolution than cgSNP, but it is less time-consuming and does not require as much computer power. Therefore, cgMLST is suitable for comparisons using large data sets (e.g., international comparison using public databases). In conclusion, screening using MLVA followed by cgMLST and cgSNP analyses would provide the highest typing resolution and improve the accuracy and cost-effectiveness of EHEC O157 surveillance. IMPORTANCE Intensive surveillance for enterohemorrhagic Escherichia coli (EHEC) serogroup O157 is important to detect outbreaks and to prevent the spread of the bacterium. Recent advances in sequencing technology made molecular surveillance using whole-genome sequence (WGS) realistic. To develop rapid, high-throughput, and cost-effective typing methods for real-time surveillance, typing resolution of WGS and a conventional typing method, multilocus variable-number tandem-repeat analysis (MLVA), was evaluated. Nation-level systematic comparison of MLVA, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) indicated that a combination of WGS and MLVA is a realistic approach to improve EHEC O157 surveillance.
Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington’s disease mice synchronous to symptoms

Abstract Motivation Huntington’s disease (HD) may evolve through gene deregulation. However, the impact of gene deregulation on the dynamics of genetic cooperativity in HD remains poorly understood. Here, we built a multi-layer network model of temporal dynamics of genetic cooperativity in the brain of HD knock-in mice (allelic series of Hdh mice). To enhance biological precision and gene prioritization, we integrated three complementary families of source networks, all inferred from the same RNA-seq time series data in Hdh mice, into weighted-edge networks where an edge recapitulates path-length variation across source-networks and age-points. Results Weighted edge networks identify two consecutive waves of tight genetic cooperativity enriched in deregulated genes (critical phases), pre-symptomatically in the cortex, implicating neurotransmission, and symptomatically in the striatum, implicating cell survival (e.g. Hipk4) intertwined with cell proliferation (e.g. Scn4b) and cellular senescence (e.g. Cdkn2a products) responses. Top striatal weighted edges are enriched in modulators of defective behavior in invertebrate models of HD pathogenesis, validating their relevance to neuronal dysfunction in vivo. Collectively, these findings reveal highly dynamic temporal features of genetic cooperativity in the brain of Hdh mice where a 2-step logic highlights the importance of cellular maintenance and senescence in the striatum of symptomatic mice, providing highly prioritized targets. Availability and implementation Weighted edge network analysis (WENA) data and source codes for performing spectral decomposition of the signal (SDS) and WENA analysis, both written using Python, are available at http://www.broca. inserm.fr/HD-WENA/. Supplementary information Supplementary data are available at Bioinformatics online.
Cytotoxic T Cells and their Activation Status are Independent Prognostic Markers in Meningiomas

Purpose: Clinically aggressive meningiomas (MGMs) are rare but treatment-resistant tumors in need for more effective therapies. Because tumor-infiltrating T lymphocytes (TILs) are essential for successful immunotherapy, we assessed TIL numbers and their activation status in primary (p-) and recurrent (r-) meningiomas and their impact on survival. Experimental Design: Presence of TILs was analyzed in 202 clinically well-annotated cases (n = 123 pMGMs and n = 79 rMGMs) focusing on higher-grade meningiomas [n = 97 World Health Organization (WHO) °II, n = 62 WHO°III]. TILs were quantified by a semiautomated analysis on whole-tissue sections stained by multicolor immunofluorescence for CD3, CD8, FOXP3, and programmed cell death protein 1 (PD-1). Results: Median T-cell infiltration accounted for 0.59% TILs per total cell count. Although there were no significant WHO°-dependent changes regarding helper (CD3+CD8−FOXP3−) and cytotoxic (CD3+CD8+FOXP3−) TILs in pMGMs, higher number of cytotoxic TILs were associated with an improved progression-free survival (PFS) independent of prognostic confounders. rMGMs were characterized by lower numbers of TILs in general, helper, and cytotoxic TILs. The additional analysis of their activation status revealed that a proportion of PD-1+CD8+ TILs within the TIL population was significantly decreased with higher WHO grade and in rMGMs. Furthermore, lower proportions of PD-1+CD8+ TILs were associated with inferior PFS in multivariate analyses, arguing for PD-1 as activation rather than exhaustion marker. Conclusions: We identified higher numbers of CD3+CD8+FOXP3− TILs and proportions of PD-1–expressing CD3+CD8+FOXP3− TILs as novel biomarkers for better survival. These findings might facilitate the selection of patients who may benefit from immunotherapy and argue in favor of an intervention in primary rather than recurrent tumors.
PD-L1 expression on nonclassical monocytes reveals their origin and immunoregulatory function

PD-L1+Ly6Clo monocytes derive from Ly6Chi monocytes in bone marrow and control T cell survival in tertiary lymphoid organs. Nonclassical Monocyte Marker Nonclassical monocytes (NCMs) are a subset of monocytes that act as sentinels in the skin endothelium and lung microvasculature. The origin of NCMs is not well understood, and Bianchini et al. now identify the immune checkpoint molecule PD-L1 as a marker that can track NCMs. Using two-photon microscopy, PD-L1+ NCMs could be tracked within the bone marrow, and contact with endosteal vessels was required for conversion from classical monocytes to NCMs. Under inflammatory conditions, PD-L1+ NCMs were found in tertiary lymphoid organs (TLOs), and expression of PD-L1 by NCMs regulated T cell survival in TLOs. Together, these findings reveal PD-L1 as a valuable tool for studying the origin and functions of NCMs. The role of nonclassical monocytes (NCMs) in health and disease is emerging, but their location and function within tissues remain poorly explored. Imaging of NCMs has been limited by the lack of an established single NCM marker. Here, we characterize the immune checkpoint molecule PD-L1 (CD274) as an unequivocal marker for tracking NCMs in circulation and pinpoint their compartmentalized distribution in tissues by two-photon microscopy. Visualization of PD-L1+ NCMs in relation to bone marrow vasculature reveals that conversion of classical monocytes into NCMs requires contact with endosteal vessels. Furthermore, PD-L1+ NCMs are present in tertiary lymphoid organs (TLOs) under inflammatory conditions in both mice and humans, and NCMs exhibit a PD-L1–dependent immunomodulatory function that promotes T cell apoptosis within TLOs. Our findings establish an unambiguous tool for the investigation of NCMs and shed light on their origin and function.
Assembly and Subcellular Localization of Bacterial Type VI Secretion Systems.

Bacteria need to deliver large molecules out of the cytosol to the extracellular space or even across membranes of neighboring cells to influence their environment, prevent predation, defeat competitors, or communicate. A variety of protein-secretion systems have evolved to make this process highly regulated and efficient. The type VI secretion system (T6SS) is one of the largest dynamic assemblies in gram-negative bacteria and allows for delivery of toxins into both bacterial and eukaryotic cells. The recent progress in structural biology and live-cell imaging shows the T6SS as a long contractile sheath assembled around a rigid tube with associated toxins anchored to a cell envelope by a baseplate and membrane complex. Rapid sheath contraction releases a large amount of energy used to push the tube and toxins through the membranes of neighboring target cells. Because reach of the T6SS is limited, some bacteria dynamically regulate its subcellular localization to precisely aim at their targets and thus increase efficiency of toxin translocation. Expected final online publication date for the Annual Review of Microbiology Volume 73 is September 9, 2019. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Fine-Grained Power Gating Using an MRAM-CMOS Non-Volatile Flip-Flop

An area-efficient non-volatile flip flop (NVFF) is proposed. Two minimum-sized Metal-Oxide-Semiconductor Field-Effect Transistor (MOSFET) and two magnetic tunnel junction (MTJ) devices are added on top of a conventional D flip-flop for temporary storage during the power-down. An area overhead of the temporary storage is minimized by reusing a part of the D flip-flop and an energy overhead is reduced by a current-reuse technique. In addition, two optimization strategies of the use of the proposed NVFF are proposed: (1) A module-based placement in a design phase for minimizing the area overhead; and (2) a dynamic write pulse modulation at runtime for reducing the energy overhead. We evaluated the proposed NVFF circuit using a compact MTJ model targeting an implementation in a 10 nm technology node. Results indicate that area overhead is 6.9% normalized to the conventional flip flop. Compared to the best previously known NVFFs, the proposed circuit succeeded in reducing the area by 4.1× and the energy by 1.5×. The proposed placement strategy of the NVFF shows an improvement of nearly a factor of 2–18 in terms of area and energy, and the pulse duration modulation provides a further energy reduction depending on fault tolerance of programs.
Custom Multiphoton/Raman Microscopy Setup for Imaging and Characterization of Biological Samples

Modern optics offers several label-free microscopic and spectroscopic solutions which are useful for both imaging and pathological assessments of biological tissues. The possibility to obtain similar morphological and biochemical information with fast and label-free techniques is highly desirable, but no single optical modality is capable of obtaining all of the information provided by histological and immunohistochemical analyses. Integrated multimodal imaging offers the possibility of integrating morphological with functional-chemical information in a label-free modality, complementing the simple observation with multiple specific contrast mechanisms. Here, we developed a custom laser-scanning microscopic platform that combines confocal Raman spectroscopy with multimodal non-linear imaging, including Coherent Anti-Stokes Raman Scattering, Second-Harmonic Generation, Two-Photon Excited Fluorescence, and Fluorescence Lifetime Imaging Microscopy. The experimental apparatus is capable of high-resolution morphological imaging of the specimen, while also providing specific information about molecular organization, functional behavior, and molecular fingerprint. The system was successfully tested in the analysis of ex vivo tissues affected by urothelial carcinoma and by atherosclerosis, allowing us to multimodally characterize of the investigated specimen. Our results show a proof-of-principle demonstrating the potential of the presented multimodal approach, which could serve in a wide range of biological and biomedical applications.
Heterostructured NiO/ZnO Nanorod Arrays with Significantly Enhanced H2S Sensing Performance

H2S gas sensors were fabricated using p-n heterojunctions of NiO/ZnO, in which the ZnO nanorod arrays were wrapped with NiO nanosheets via a hydrothermal synthesis method. When the H2S gas molecules were adsorbed and then oxidized on the ZnO surfaces, the free electrons were released. The increase in the electron concentration on the ZnO boosts the transport speed of the electrons on both sides of the NiO/ZnO p-n junction, which significantly improved the sensing performance and selectivity for H2S detection, if compared with sensors using the pure ZnO nanorod arrays. The response to 20 ppm of H2S was 21.3 at 160 °C for the heterostructured NiO/ZnO sensor, and the limit of detection was 0.1 ppm. We found that when the sensor was exposed to H2S at an operating temperature below 160 °C, the resistance of the sensor significantly decreased, indicating its n-type semiconductor nature, whereas when the operating temperature was above 160 °C, the resistance significantly increased, indicating its p-type semiconductor nature. The sensing mechanism of the NiO/ZnO heterostructured H2S gas sensor was discussed in detail.