Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of Alignment on People's Ability to Judge Event Sequence Similarity

Event sequences are central to the analysis of data in domains that range from biology and health, to logfile analysis and people's everyday behavior. Many visualization tools have been created for such data, but people are error-prone when asked to judge the similarity of event sequences with basic presentation methods. This article describes an experiment that investigates whether local and global alignment techniques improve people's performance when judging sequence similarity. Participants were divided into three groups (basic versus local versus global alignment), and each participant judged the similarity of 180 sets of pseudo-randomly generated sequences. Each set comprised a target, a correct choice and a wrong choice. After training, the global alignment group was more accurate than the local alignment group (98 versus 93 percent correct), with the basic group getting 95 percent correct. Participants’ response times were primarily affected by the number of event types, the similarity of sequences (measured by the Levenshtein distance) and the edit types (nine combinations of deletion, insertion and substitution). In summary, global alignment is superior and people's performance could be further improved by choosing alignment parameters that explicitly penalize sequence mismatches.
Unusual $C$ – $V$ Characteristics of High-Resistivity SOI Wafers

The maximum capacitance for bulk or Silicon on Insulator (SOI) wafers is governed by the gate/contact area. During our capacitance-voltage (C-V) characterization of high-resistivity SOI wafers with Al contacts directly on the Si film, we observed the maximum capacitance to be much higher than that due to the contact area, suggesting bias spreading due to the distributed transmission line of the film resistance and buried oxide capacitance. In addition, an “S”-shape C-V plot was observed in the accumulation region.
Same Game, Different Players: Emerging Pathogens of the CF Lung

Incidences of non-tuberculosis mycobacteria (NTM) and Aspergillus fumigatus have increased around the world over the past decade and have become a significant health threat to immunocompromised individuals such as those with cystic fibrosis (CF). CF is characterized by the buildup of mucus in the lungs which become chronically infected by a myriad of pathogens. ABSTRACT The survival rates of individuals with cystic fibrosis (CF) have significantly increased as a result of improved therapies, such as the inclusion of cystic fibrosis transmembrane conductance regulator (CFTR) modulators for some mutations. However, microbial infection of the airways remains a significant clinical problem. The well-known pathogens Pseudomonas aeruginosa and Staphylococcus aureus continue to establish difficult-to-treat infections in the CF lung. However, in recent years, there has been an increased prevalence of both Aspergillus fumigatus (Af) and non-tuberculous mycobacteria (NTM) species isolated from CF patient sputa. The emergence of these pathogens opens an important area of discussion about multikingdom infections, specifically, how interspecies interactions have the potential to shape the course of infection, such as tolerance to host immune defenses and antimicrobial therapies. Their ability to establish themselves in an existing polymicrobial environment suggests to us that microbial interactions play a significant role, and characterizing these mechanisms and understanding their implications will be critical to the future development of better antimicrobial therapies. With this minireview, we hope to inspire conversations about and demonstrate the merit of more research in this area. IMPORTANCE Incidences of non-tuberculous mycobacteria (NTM) and Aspergillus fumigatus have increased around the world over the past decade and have become a significant health threat to immunocompromised individuals such as those with cystic fibrosis (CF). CF is characterized by the buildup of mucus in the lungs which become chronically infected by a myriad of pathogens. The emergence of these pathogens in established infection sites raises many questions about the microbial ecosystems they become a part of, specifically how changes in these ecosystems impact disease outcomes. Understanding how microbial communities establish and maintain themselves despite medical treatment and host immune defenses will be critical for the development of improved therapeutic strategies.
Thaumatin-Like Protein (Pru av 2) Is a Cherry Allergen That Triggers Percutaneous Sensitization in Mice

Numerous recent studies have suggested that food allergens enter the skin and predispose individuals to food allergies through the production of IgE antibodies in the body. Cherries are a popular fruit eaten worldwide. However, cherries are an allergenic food and percutaneous sensitization with cherry allergens through the perioral region may occur while ingesting cherries. The identity of the cherry protein that triggers percutaneous sensitization in humans or animal models remains unknown. In this study, the backs of BALB/c mice were shaved and crude cherry extracts containing sodium dodecyl sulfate were applied to the skin. Thereafter, the cherry-specific IgE and IgG1 antibodies generated and secreted in response to the epidermal application were measured using an enzyme-linked immunosorbent assay or immunoblotting. Skin exposure to cherry extracts elevated cherry-specific IgG1 levels. Application of fractionated and purified cherry proteins (antigen candidates for percutaneous sensitization) that bound to the IgG1 antibodies led to the identification of a thaumatin-like protein (Pru av 2). This molecule is known as the major cherry allergen that affects humans. In conclusion, our study identified Pru av 2 as a cherry allergen that triggers percutaneous sensitization in mice for the first time.
Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea

Abstract Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.
HIV-Infected Patients: Cross Site-Specific Hydrolysis of H3 and H4 Histones and Myelin Basic Protein with Antibodies against These Three Proteins

Histones play important roles in chromatin functioning and gene transcription, but in the intercellular space, they are harmful since they stimulate systemic inflammatory and toxic responses. Electrophoretically homogeneous IgGs against myelin basic protein (MBP), as well as H3 and H4 histones, were isolated from sera of HIV-infected patients. In contrast to known classical proteases, these IgGs split exclusively only histones and MBP but no other control proteins. Among 13 sites of hydrolysis of H3 by IgGs against H3 and 14 sites for anti-MBP IgGs, only two sites of the hydrolysis were the same. Between seven cleavage sites of H4 with IgGs against H4 and 9 sites of this histone hydrolysis by antibodies against MBP, only three sites were the same. The sites of hydrolysis of H3 (and H4) with abzymes against these histones and against MBP were different, but several expended protein clusters containing hydrolysis sites are partially overlapped. The existence of enzymatic cross-reactivity of abzymes against H3 and H4 and MBP represents a great menace to humans since due to cell apoptosis, histones constantly occur in human blood. They can hydrolyze MBP of the myelin sheath of axons and play a negative role in the pathogenesis of HIV-infected patients.
Laboratory Operando XAS Study of Sodium Iron Titanite Cathode in the Li-Ion Half-Cell

Electrochemical characterization of the novel sodium iron titanate Na0.9Fe0. 45Ti1.55O4 was performed upon cycling in the Li-ion half-cell. The material exhibited stable cycling in the voltage range 2–4.5 V, and the number of alkali ions extracted per formula unit was approximately half of the Na stoichiometry value. Using laboratory X-ray absorption spectrometry, we measured operando Fe K-edge X-ray absorption spectra in the first 10 charge–discharge cycles and quantified the portion of charge associated with the transition metal redox reaction. Although 3d metals are commonly accepted redox-active centers in the intercalation process, we found that in all cycles the amount of oxidized and reduced Fe ions was almost 20% less than the total number of transferred electrons. Using density functional theory (DFT) simulations, we show that part of the reversible capacity is related to the redox reaction on oxygen ions.
The respiratory occlusion discrimination task: A new paradigm to measure respiratory interoceptive accuracy.

Interoception, or the sense of the internal state of the body, is hypothesized to be essential for a wide range of psychobiological processes and the development and perpetuation of several (mental) health problems. However, the study of interoceptive accuracy, the objectively measured capacity to detect or discriminate conscious bodily signals, has been hampered by the use of tasks with questionable construct validity and is often limited to studying interoception solely in the cardiac domain. We developed a novel task to measure interoceptive accuracy in the respiratory domain, the respiratory occlusion discrimination (ROD) task. In this task, interoceptive accuracy is defined as an individual's ability to detect small differences in lengths of short respiratory occlusions, assessed by means of an adaptive staircase procedure. This article describes a validation study (N = 97) aimed at investigating the internal consistency, test-retest reliability, and discriminant validity of the ROD task. The average just noticeable difference of lengths of respiratory occlusion was 74.22 ms, with large inter-individual variability (SD = 37.1 ms). The results of the validation study indicate acceptable internal consistency (Cronbach's alpha = 0.70), 1-week test-retest reliability (r = 0.53), and discriminant validity, as indicated by a lack of correlation between the ROD task and an auditory discrimination task with identical design (r = 0.18), and a weak correlation with breathing behavior (r = -0.27). The ROD task is a promising novel paradigm to study interoceptive accuracy and its role in various psychobiological processes and disorders.
Canadian Consensus for Biomarker Testing and Treatment of TRK Fusion Cancer in Pediatric Patients

Neurotrophic tyrosine receptor kinase gene fusions (NTRK) are oncogenic drivers present at a low frequency in most tumour types (<5%), and at a higher frequency (>80%) in a small number of rare tumours (e.g., infantile fibrosarcoma [IFS]) and considered mutually exclusive with other common oncogenic drivers. Health Canada recently approved two tyrosine receptor kinase (TRK) inhibitors, larotrectinib (for adults and children) and entrectinib (for adults), for the treatment of solid tumours harbouring NTRK gene fusions. In Phase I/II trials, these TRK inhibitors have demonstrated promising overall response rates and tolerability in patients with TRK fusion cancer who have exhausted other treatment options. In these studies, children appear to have similar responses and tolerability to adults. In this report, we provide a Canadian consensus on when and how to test for NTRK gene fusions and when to consider treatment with a TRK inhibitor for pediatric patients with solid tumours. We focus on three pediatric tumour types: non-rhabdomyosarcoma soft tissue sarcoma/unspecified spindle cell tumours including IFS, differentiated thyroid carcinoma, and glioma. We also propose a tumour-agnostic consensus based on the probability of the tumour harbouring an NTRK gene fusion. For children with locally advanced or metastatic TRK fusion cancer who have either failed upfront therapy or lack satisfactory treatment options, TRK inhibitor therapy should be considered.
Implications of land ecosystem-atmosphere interactions for strategies for climate change adaptation and mitigation

The standard approach to predicting climate change, assessing its impacts and planning mitigation strategies tends to be compartmentalized, leading to inadequate or incomplete advice for climate policy. Climate models used for future global warming predictions and attribution of past changes generally consider only global climate drivers, ignoring local drivers, such as land use change and urban effects. Impacts studies are generally carried out in isolation from each other and hence ignore interactions between different impacts sectors, such as hydrology, natural ecosystems and agriculture. Feedbacks from impacts to climate change, which often involve land ecosystem-atmosphere interactions, are often neglected. This can result in representations of global changes that are at best inconsistent and at worst completely misleading. Moreover, a number of climate change mitigation strategies, such as carbon sequestration and biofuels involve changes in land ecosystems. In addition to affecting climate through the exchange of carbon with the atmosphere, these land ecosystem changes may affect climate change or its impacts through a variety of additional processes, such as surface albedo change or changes in the surface moisture budget. Failure to account for these may have consequences that are potentially at odds with the aims of climate change mitigation.
Comprehensive Hydrodynamic Investigation of Zebrafish Tail Beats in a Microfluidic Device with a Shape Memory Alloy

The zebrafish is acknowledged as a reliable species of choices for biomechanical-related investigations. The definite quantification of the hydrodynamic flow physics caused by behavioral patterns, particularly in the zebrafish tail beat, is critical for a comprehensive understanding of food toxicity in this species, and it can be further interpreted for possible human responses. The zebrafish’s body size and swimming speed place it in the intermediate flow regime, where both viscous and inertial forces play significant roles in the fluid–structure interaction. This pilot work highlighted the design and development of a novel microfluidic device coupled with a shape memory alloy (SMA) actuator to immobilize the zebrafish within the observation region for hydrodynamic quantification of the tail-beating behavioral responses, which may be induced by the overdose of food additive exposure. This study significantly examined behavioral patterns of the zebrafish in early developmental stages, which, in turn, generated vortex circulation. The presented findings on the behavioral responses of the zebrafish through the hydrodynamic analysis provided a golden protocol to assess the zebrafish as an animal model for new drug discovery and development.
A New Dromaeosaurid from the Late Cretaceous Khulsan Locality of Mongolia

ABSTRACT A new dromaeosaurid dinosaur, Shri devi, from the Late Cretaceous deposit of the Barun Goyot Formation at Khulsan, Mongolia, is described here. The Barun Goyot Formation (herein referred to as the Barun Goyot) is stratigraphically intermediate between the overlying Nemegt Formation and the underlying Djadokhta Formation, where much of the dromaeosaurid diversity has been reported to date. Sediments of the Barun Goyot are typically considered Upper Campanian in age. Although dromaeosaurid remains have been noted to occur in the Barun Goyot for decades, descriptive and taxonomic work has never been completed for the material. The holotype specimen (IGM 100/980) consists of a partially articulated individual preserving the right hind limb; left tibiotarsus; pelvis; and adjacent cervical, dorsal, and caudal vertebrae. IGM 100/980 is referable to a clade with Velociraptor based on the presence of a distinct ambiens tubercle located proximally on the anterior face of the pubis, a well-developed anterior tuberosity proximally located on the ischium, and a rounded longitudinal ischial ridge. It is distinguishable from V. mongoliensis based on a weak fourth trochanter (shared with all other dromaeosaurids) and deep anterior pedicular fossae in the cervical vertebrae; epipophyses in the last four cervicals are not raised but are instead represented by rugose circular scars. A suite of axial and appendicular characters are diagnostic for the new species. New discoveries including Shri devi allow for an improved understanding of dromaeosaurid anatomy, as well as the temporal and regional variation of the dromaeosaurid fauna of Mongolia and Inner Mongolia (Nei Mongol Autonomous Region, China), during the Late Cretaceous.
Heightened resistance to host type 1 interferons characterizes HIV-1 at transmission and after antiretroviral therapy interruption

Interferon-mediated pressures vary throughout HIV-1 infection but are the highest during viral rebound after treatment interruption. Putting pressure on HIV Type 1 interferons provide early host immune defense against viruses, including HIV-1, by promoting expression of proteins that have direct or indirect antiviral activity. It remains unclear how viruses that persist long term, such as HIV-1, escape type 1 interferon–mediated pressure. Gondim et al. characterize interferon resistance in HIV-1 isolates acquired from HIV-1–infected individuals over several years. The authors found that HIV-1 isolates acquired at the time of initial infection or during interruption of antiretroviral therapy were the most resistant to type 1 interferons. These findings underpin the importance of type 1 interferons in controlling HIV-1 infection in the host. Type 1 interferons (IFN-I) are potent innate antiviral effectors that constrain HIV-1 transmission. However, harnessing these cytokines for HIV-1 cure strategies has been hampered by an incomplete understanding of their antiviral activities at later stages of infection. Here, we characterized the IFN-I sensitivity of 500 clonally derived HIV-1 isolates from the plasma and CD4+ T cells of 26 individuals sampled longitudinally after transmission or after antiretroviral therapy (ART) and analytical treatment interruption. We determined the concentration of IFNα2 and IFNβ that reduced viral replication in vitro by 50% (IC50) and found consistent changes in the sensitivity of HIV-1 to IFN-I inhibition both across individuals and over time. Resistance of HIV-1 isolates to IFN-I was uniformly high during acute infection, decreased in all individuals in the first year after infection, was reacquired concomitant with CD4+ T cell loss, and remained elevated in individuals with accelerated disease. HIV-1 isolates obtained by viral outgrowth during suppressive ART were relatively IFN-I sensitive, resembling viruses circulating just before ART initiation. However, viruses that rebounded after treatment interruption displayed the highest degree of IFNα2 and IFNβ resistance observed at any time during the infection course. These findings indicate a dynamic interplay between host innate responses and the evolving HIV-1 quasispecies, with the relative contribution of IFN-I to HIV-1 control affected by both ART and analytical treatment interruption. Although elevated at transmission, host innate pressures are the highest during viral rebound, limiting the viruses that successfully become reactivated from latency to those that are IFN-I resistant.
The Effect of Forbush Decreases on the Polar-Night HO x Concentration Affecting Stratospheric Ozone

It is well-known that energetic particle precipitations during solar proton events increase ionization rates in the middle atmosphere enhancing the production of hydrogen oxide radicals (HO x ) involved in the catalytic ozone destruction cycle. There are many studies where the contribution of energetic particles to the formation of hydrogen oxide radicals and ozone loss has been widely investigated. However, until now, there was no solid evidence that the reduction in galactic cosmic ray fluxes during a magnetic storm, known as Forbush-effect, directly and noticeably affects the polar-night stratospheric chemistry. Here, the impact of the Forbush decrease on the behavior of hydrogen oxide radicals was explored using the chemistry-climate model SOCOLv2. We found that hydrogen oxide radical lost about half of its concentration over the polar boreal night stratosphere owing to a reduction in ionization rates caused by Forbush decreases after solar proton events occurred on 17 and 20 of January 2005. The robust response in ozone was not found. There is not any statistically significant response in (NO x ) on Forbush decrease events as well as over summer time in the southern polar region. The results of this study can be used to increase the veracity of ozone loss estimation if stronger Forbush events can have place.
Asomatognosia: Structured Interview and Assessment of Visuomotor Imagery

Asomatognosia designates the experience that one’s body has faded from awareness. It is typically a somaesthetic experience but may target the visual modality (“asomatoscopy”). Frequently associated symptoms are the loss of ownership or agency over a limb. Here, we elaborate on the rigorous nosographic classification of asomatognosia and introduce a structured interview to capture both its core symptoms and associated signs of bodily estrangement. We additionally report the case of a pure left-sided hemiasomatognosia occurring after surgical removal of a meningioma in the right atrium. Despite the wide lesions of the right angular gyrus and of the temporo-parietal junction, the patient did not present visuospatial deficits or bodily awareness disorders other than hemiasomatognosia. The patient and 10 matched controls’ motor imagery was formally assessed with a limb laterality task in which they had to decide whether hands and feet presented under different angles of rotation depicted a left or a right limb. Bayesian statistics showed that patient’s reaction times were significantly impaired exclusively for the left foot and especially for mental rotations requiring somatomotor rather than visual limb representations. This was in accordance with a more enduring left-sided hemiasomatognosia for the lower limbs confined to the somesthetic modality. Our findings shed new light on motor imagery in asomatognosia and encourage the future use of the structured interview introduced here. In addition, the limb laterality task may capture phenomenological elements of a case by chronometric means. This allows a more standardized reporting of phenomenological detail and improves communication across different clinical facilities.