Miracle-dz/UniFAR-FTUs huggingface dataset:
DCNS: Automated Detection Of Conservative Non-Sleep Defects in the Linux Kernel

For waiting, the Linux kernel offers both sleep-able and non-sleep operations. However, only non-sleep operations can be used in atomic context. Detecting the possibility of execution in atomic context requires a complete inter-procedural flow analysis, often involving function pointers. Developers may thus conservatively use non-sleep operations even outside of atomic context, which may damage system performance, as such operations unproductively monopolize the CPU. Until now, no systematic approach has been proposed to detect such conservative non-sleep (CNS) defects. In this paper, we propose a practical static approach, named DCNS, to automatically detect conservative non-sleep defects in the Linux kernel. DCNS uses a summary-based analysis to effectively identify the code in atomic context and a novel file-connection-based alias analysis to correctly identify the set of functions referenced by a function pointer. We evaluate DCNS on Linux 4.16, and in total find 1629 defects. We manually check 943 defects whose call paths are not so difficult to follow, and find that 890 are real. We have randomly selected 300 of the real defects and sent them to kernel developers, and 251 have been confirmed.
The crystal structure of an antiparallel chair-type G-quadruplex formed by Bromo-substituted human telomeric DNA

Abstract Human telomeric guanine-rich DNA, which could adopt different G-quadruplex structures, plays important roles in protecting the cell from recombination and degradation. Although many of these structures were determined, the chair-type G-quadruplex structure remains elusive. Here, we present a crystal structure of the G-quadruplex composed of the human telomeric sequence d[GGGTTAGG8GTTAGGGTTAGG20G] with two dG to 8Br-dG substitutions at positions 8 and 20 with syn conformation in the K+ solution. It forms a novel three-layer chair-type G-quadruplex with two linking trinucleotide loops. Particularly, T5 and T17 are coplanar with two water molecules stacking on the G-tetrad layer in a sandwich-like mode through a coordinating K+ ion and an A6•A18 base pair. While a twisted Hoogsteen A12•T10 base pair caps on the top of G-tetrad core. The three linking TTA loops are edgewise and each DNA strand has two antiparallel adjacent strands. Our findings contribute to a deeper understanding and highlight the unique roles of loop and water molecule in the folding of the G-quadruplex.
Preschool screen-media usage predicts mental imagery two years later

ABSTRACT During typical childhood interactions with screen-media, two features are prominent. First, input is dominated by audio-visual signals and second, these predominately provide children with ready-made images, potentially negating effortful mental imagery construction. We present a two-year longitudinal study on a sample of 109 preschool children. We endeavoured to measure media usage and mental imagery development in a differentiated manner, also taking account of control variables and purpose of media use (learning vs. entertainment). Results indicated that children who viewed more media had worse mental imagery skill. Active media usage (e.g. gaming, tablets) and total screen time linked to lower mental imagery performance. Further, both mental images in the visual and haptic modalities appeared equally affected. Findings are discussed in terms of shaping early educational experiences with respect to virtual and three dimensional reality.
Organs to Cells and Cells to Organoids: The Evolution of in vitro Central Nervous System Modelling

With 100 billion neurons and 100 trillion synapses, the human brain is not just the most complex organ in the human body, but has also been described as “the most complex thing in the universe. ” The limited availability of human living brain tissue for the study of neurogenesis, neural processes and neurological disorders has resulted in more than a century-long strive from researchers worldwide to model the central nervous system (CNS) and dissect both its striking physiology and enigmatic pathophysiology. The invaluable knowledge gained with the use of animal models and post mortem human tissue remains limited to cross-species similarities and structural features, respectively. The advent of human induced pluripotent stem cell (hiPSC) and 3-D organoid technologies has revolutionised the approach to the study of human brain and CNS in vitro, presenting great potential for disease modelling and translational adoption in drug screening and regenerative medicine, also contributing beneficially to clinical research. We have surveyed more than 100 years of research in CNS modelling and provide in this review an historical excursus of its evolution, from early neural tissue explants and organotypic cultures, to 2-D patient-derived cell monolayers, to the latest development of 3-D cerebral organoids. We have generated a comprehensive summary of CNS modelling techniques and approaches, protocol refinements throughout the course of decades and developments in the study of specific neuropathologies. Current limitations and caveats such as clonal variation, developmental stage, validation of pluripotency and chromosomal stability, functional assessment, reproducibility, accuracy and scalability of these models are also discussed.
Performance analysis of co-operative MIMO channel over sensor control networks

In cooperative networks, to reduce the interference communication among the coordination of cells a relays setup introduced between multiple inputs multiple output (MIMO) designs. In this paper, Cooperative MIMO (C-MIMO) is utilized for efficient energy technologies. For sake of best performance of Wireless the sensor Networks (WSNs), the bit inter-leaved coded modulation (BICM) and bit inter-leaved coded modulation with iterative decoding (BICM-ID) code are utilized. The simulation results demonstrate that for BICM and BICM-ID the cooperative communication scheme exceeds the single input single output (SISO) technique. Under the different statistical distributions over the WSNs the bit error rate (BER) is analyzed for the system.
Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts

Modulating gut microbiota to promote host health is well recognized. Therefore, people consume dietary products containing traditional probiotics in wishing to improve their health, and they need more research-based advices on how to select products with suitable probiotic species. Probiotic designers are sometimes confused about how to design precision products for different consumers by taking advantages of different probiotic species’ strengths. Additionally, large-scale analyses on traditional probiotic complementarity potentials and their roles in gut microbiome related to common diseases are not well understood. Here, we comprehensively analyzed 444 genomes of major traditional probiotic (sub) species (MTPS, n = 15) by combining one newly sequenced genome with all of the public NCBI-available MTPS-related genomes. The public human fecal metagenomic data (n = 1,815) of eight cohorts were used to evaluate the roles of MTPS, compared to other main gut bacteria, in disease association by examining the species enrichment direction in disease group or the control group. Our work provided a comprehensive genetic landscape and complementarity relations for MTPS and shed light on personalized probiotic supplements for consumers with different health status and the necessity that researchers and manufactures could explore novel probiotics as well as traditional ones.
NF-κB Signaling in Macrophages: Dynamics, Crosstalk, and Signal Integration

The nuclear factor-κB (NF-κB) signaling pathway is one of the best understood immune-related pathways thanks to almost four decades of intense research. NF-κB signaling is activated by numerous discrete stimuli and is a master regulator of the inflammatory response to pathogens and cancerous cells, as well as a key regulator of autoimmune diseases. In this regard, the role of NF-κB signaling in immunity is not unlike that of the macrophage. The dynamics by which NF-κB proteins shuttle between the cytoplasm and the nucleus to initiate transcription have been studied rigorously in fibroblasts and other non-hematopoietic cells, but many questions remain as to how current models of NF-κB signaling and dynamics can be translated to innate immune cells such as macrophages. In this review, we will present recent research on the dynamics of NF-κB signaling and focus especially on how these dynamics vary in different cell types, while discussing why these characteristics may be important. We will end by looking ahead to how new techniques and technologies should allow us to analyze these signaling processes with greater clarity, bringing us closer to a more complete understanding of inflammatory transcription factor dynamics and how different cellular contexts might allow for appropriate control of innate immune responses.
Consecutive Slides on Axial View Is More Effective Than Transversal Diameter to Differentiate Mechanisms of Single Subcortical Infarctions in the Lenticulostriate Artery Territory

Objective: Lipohyalinosis or atherosclerosis might be responsible for single subcortical infarctions (SSIs); however, ways of differentiating between the two clinically remain uncertain. We aimed to investigate whether consecutive slides on axial view or transversal diameter is more effective to differentiate mechanisms by comparing their relationships with white matter hyperintensities (WMHs). Methods: All the participants from the Standard Medical Management in Secondary Prevention of Ischemic stroke in China (SMART) cohort who had SSIs in the lenticulostriate artery territory were included and categorized according to consecutive slides on axial view (≥4 consecutive slices or not) and transversal diameter (≥15 mm or not). The associations between the severity of WMHs and the different categories were analyzed. Results: Among the 3,821 patients of the SMART study, 281 had diffusion-weighted image-proven SSIs in the lenticulostriate artery territory. When classified by consecutive slides on axial view, SSIs on ≥4 slices were significantly associated with the severity of the WMHs, both in deep WMH (DWMH) (odds ratio [OR], 0.32; 95% confidence interval [CI], 0.11–0.97; p = 0.04) and periventricular hyperintensity (PVH) (OR, 0.37; 95% CI, 0.17–0.78; p = 0.01). No such association was found on the basis of the transversal diameter (p > 0.1). Conclusion: Consecutive slides on axial view (≥4 consecutive slices) might be more effective than transversal diameter to identify the atherosclerotic mechanisms of SSIs in the lenticulostriate artery territory. Clinical Trial Registration: http://www.clinicaltrials. gov. Unique identifier: NCT00664846
Investigation of the anti-tumor effects of bevacizumab on glioblastoma cells

Investigation of The Anti-Tumor Effects of Bevacizumab on Glioblastoma CellJ Basic Clin ABSTRACT Aim: Glioblastoma multiforme (GBM) is the most malignant glial tumor. Angiogenesis which provides nutrient and oxygen support to proliferating cells plays an essential role in GBM development, proliferation, and metastasis. The development of antiangiogenetic agents is a promising treatment approach as blood vessels are essential for the vitality of tumor cells. For this purpose, in this study, the effects of bevacizumab on cell viability and apoptosis were analyzed using glioblastoma cells. Material and method: U-87 MG and T98G cells were treated with various concentrations of bevacizumab for 24 hours, 48 hours, and 72 hours. Cell viability was analyzed after administration of bevacizumab. Cytotoxicity was determined using MTT. Apoptosis rate was determined with cell death detection kit. Results: Cell viability analysis showed that when 8 mg / ml bevacizumab was administered to glioblastoma cells for 48 hours and 72 hours, cell proliferation was only 50% compared to proliferation of cells without bevacizumab. Additionally, apoptosis rates for U-87 MG and T98G cell lines treated with various concentrations of bevacizumab for 48 hours and 72 hours showed results similar to those of cell viability. Conclusions: This study showed that while high concentration treatment of U-87 MG cells caused an increase in cell viability in a time-dependent manner, high dose treatment of T98G cells resulted in a decrease in cell viability in a time-dependent manner. This means that some glioblastoma cells can still survive under high doses of bevacizumab. This, in turn, demonstrated that glioblastoma cells developed resistance against bevacizumab.
Effectiveness of Workplace Intervention for Reducing Alcohol Consumption: a Systematic Review and Meta-Analysis.

AIMS To review the effectiveness of workplace interventions in reducing alcohol consumption among employees. METHODS Systematic search of science databases from inception till May 2018 for trials where an intervention was tested against a control and data presented as amount of alcohol consumed per week. Quality of trials was assessed by Cochrane risk of bias tool. Meta-analysis was performed with random-effects model and pooled mean difference (MD) was reported with 95% confidence interval. Publication bias was assessed using Egger's test. RESULTS Seven trials with 1291 participants could be included. No outcome assessments were blinded. There was positive effect of workplace intervention on reduction of alcohol consumption with pooled MD of -2.25 [95% CI: -4.20 to -0.30]. The effect was only seen where subjects had a baseline alcohol consumption of over 15 standard drinks per week. There was no heterogeneity across the trials (I2=0%). Funnel plot was symmetrical shaped and Egger's test confirmed that there was no publication bias. Two studies found no advantages to intervention on differences on the AUDIT test. CONCLUSION There is weak evidence for workplace interventions (varying modes) as a way of facilitating reduction in the consumption of alcohol among employees but only among the heavier consumers.
A comparative analysis of protocols for IoT network management

The complexity and growth of new smart objects networks are generating a new demand for the maintenance of these devices, with the need to remotely monitor and control these devices without consuming significant resources. Analyzing the memory and electric power consumption of the protocols used in the management of these networks is a way to highlight the best protocol alternatives for this type of application. This study develops an experimental study, analyzing the behavior of SNMP, Zabbix, and MQTT protocols, in terms of memory and electric power consumption, when it is used in an Internet of Things application, with a sensor device implemented on the ESP8266. The experiment is performed by monitoring devices in an environment with some Motes and a Zabbix server. The study analyzes the ROM and RAM memories occupied by the firmware code, in addition to the electric power consumption of each protocol. At the end, the study confirms that the three protocols analyzed are supported by the platform used. The research shows that the SNMP is the protocol that consumes the least amount of device memory, that there is no significant difference in the energy consumption between the protocols, and that the MQTT protocol is suitable to be used in this environment and it also enables a significant reduction in energy consumption.
ScissorGC: scalable and efficient compaction for Java full garbage collection

Java runtime frees applications from manual memory management through automatic garbage collection (GC). This, however, is usually at the cost of stop-the-world pauses. State-of-the-art collectors leverage multiple generations, which will inevitably suffer from a full GC phase scanning and compacting the whole heap. This induces a pause tens of times longer than normal collections, which largely affects both throughput and latency of applications. In this paper, we comprehensively analyze the full GC performance of the Parallel Scavenge garbage collector in HotSpot. We find that chain-like dependencies among heap regions cause low thread utilization and poor scalability. Furthermore, many heap regions are filled with live objects (referred to as dense regions), which are unnecessary to collect. To address these two problems, we provide , which contains two main optimizations: dynamically allocating shadow regions as compaction destinations to eliminate region dependencies and skipping dense regions to reduce GC workload. Evaluation results against the HotSpot JVM of OpenJDK 8/11 show that works on most benchmarks and leads to 5.6X/5.1X improvement at best in full GC throughput and thereby boost the application performance by up to 61.8%/49.0%.
Userland CO-PAGER: boosting data-intensive applications with non-volatile memory, userspace paging

With the emergence of low-latency non-volatile memory (NVM) storage, the software overhead, incurred by the operating system, becomes more prominent. The Linux (monolithic) kernel, incorporates a complex I/O subsystem design, using redundant memory copies and expensive user/kernel context switches to perform I/O. Memory-mapped I/O, which internally uses demand paging, has recently become popular when paired with low-latency storage. It improves I/O performance by mapping the data DMA transfers directly to userspace memory and removing the additional data copy between user/kernel space. However, for data-intensive applications, when there is insufficient physical memory, frequent page faults can still trigger expensive mode switches and I/O operations. To tackle this problem, we propose CO-PAGER, which is a lightweight userspace memory service. CO-PAGER consists of a minimal kernel module and a userspace component. The userspace component handles (redirected) page faults, performs memory management and I/O operations and accesses NVM storage directly. The kernel module is used to update memory mapping between user and kernel space. In this way CO-PAGER can bypass the deep kernel I/O stacks and provide a flexible/customizable and efficient memory paging service in userspace. We provide a general programming interface to use the CO-PAGER service. In our experiments, we also demonstrate how the CO-PAGER approach can be applied to a MapReduce framework and improves performance for data-intensive applications.
Sunscreen mucilage: a photoprotective adaptation found in terrestrial green algae (Zygnematophyceae)

Abstract Terrestrial microalgae evolved a variety of photoprotective strategies enabling a life on land. This includes the production of sunscreen compounds, which shield cells from excess radiation. Here, we report a new genus of conjugating green algae, Serritaenia gen. nov., whose members produce extracellular mucilage with a striking pigmentation. This phenomenon is very unusual for eukaryotic algae and poses cell biological and functional questions. So far, extracellular sunscreen pigments are exclusively known from cyanobacteria, while eukaryotic algae typically contain intracellular sunscreens. We demonstrate that pigmented mucilage in Serritaenia spp. can be induced by experimental exposure to UVB in an intensity-dependent manner, and that it strongly absorbs deleterious wavebands. Microscopic details of UVR-treated cells suggest that the directional secretion of pigmented mucilage is responsible for the defined and well-oriented pigment layers observed in natural material. Even though the chemical nature of the pigment remains to be elucidated, several pieces of evidence suggest that the ‘sunscreen mucilage’ of Serritaenia represents an elaborate photoprotective adaptation, unprecedented in eukaryotic algae.
Low Intensity Extracorporeal Shock Wave Therapy as a Novel Treatment for Stress Urinary Incontinence: A Randomized-Controlled Clinical Study

Background and Objectives: To evaluate the effects of low intensity extracorporeal shock wave therapy (LiESWT) on stress urinary incontinence (SUI). Materials and Methods: This investigation was a multicenter, single-blind, randomized-controlled trial study. Sixty female SUI patients were randomly assigned to receive LiESWT with 0.25 mJ/mm2 intensity, 3000 pulses, and 3 pulses/s, once weekly for a 4-week (W4) and 8-week (W8) period, or an identical sham LiESWT treatment without energy transmission. The primary endpoint was the changes in urine leakage as measured by a pad test and validated standardized questionnaires, while the secondary endpoint was the changes in a 3-day urinary diary among the baseline (W0), the W4 and W8 of LiESWT, and 1-month (F1), 3-month (F3), and 6-month (F6) follow-up after LiESWT. Results: The results showed that 4 weeks of LiESWT could significantly decrease urine leakage based on the pad test and validated standardized questionnaire scores, as compared to the sham group. Moreover, 8 weeks of LiESWT could significantly reduce urine leakage but increase urine volume and attenuate urgency symptoms, which showed meaningful and persistent improvement at W8, F1, F3, and F6. Furthermore, validated standardized questionnaire scores were significantly improved at W8, F1, F3, and F6 as compared to the baseline (W0). Conclusions: Eight weeks of LiESWT attenuated SUI symptoms upon physical activity, reduced urine leakage, and ameliorated overactive bladder symptoms, which implied that LiESWT significantly improved the quality of life. Our findings suggested that LiESWT could serve as a potentially novel and non-invasive treatment for SUI.
Current Controversy: Spikes, Bursts, and Synchrony in Generalized Absence Epilepsy: Unresolved Questions Regarding Thalamocortical Synchrony in Absence Epilepsy

Absence epilepsy is a disorder of thalamocortical networks. Animal models have provided detailed information regarding the core cellular, synaptic, and network features that contribute to the electroencephalogram spike and wave discharge characteristic of typical absence epilepsy. Understanding of seizure networks and dynamics is a critical step toward improving treatments, yet competing conceptual models have evolved to explain seizure initiation and propagation. Recent studies have questioned 2 key model concepts: (1) T-type Ca2+ channel-dependent burst firing in thalamic relay neurons may not be essential for seizure generation, bringing into question the proposed mechanism for the antiepileptic drug ethosuximide in reducing thalamic bursting and (2) widespread synchronized neural activity may not be a core feature of the seizures, indicating that reductions in synchrony would not be a productive therapeutic goal. In this review, I will discuss these current findings, highlight the innovative approaches that have enabled these insights, and provide a unified framework that incorporates these sometimes-conflicting ideas. Finally, I lay out future work that will be necessary to finally resolve the remaining issues.
Race, relational dynamics and anxious adjustments: the complexities of identities in relation to one another

ABSTRACT Positionality statements, or statements acknowledging relevant background, context, and situatedness of researcher positions and identities are widely used in qualitative research. In recent years, public claims of insider status have been contested by the communities in question, often popularized in mainstream media. This article explores the complexities and factors that influence the way researchers think about their own positionality in relation to their participants, using written reflections on race and positional dynamics, as well as relevant literature. Through this article, I explore these complexities and the underlying motivations that compel me to present my location, identity, or positionality in particular ways. These reflections are valuable for provoking critical reflection about the way we interpret our own identities in relation to one another, and the reasons we may do so.