Miracle-dz/UniFAR-FTUs huggingface dataset:
BabA-mediated adherence of pediatric ulcerogenic H. pylori strains to gastric mucins at neutral and acidic pH

ABSTRACT Helicobacter pylori infection can result in non-ulcer dyspepsia (NUD), peptic ulcer disease (PUD), adenocarcinoma, and gastric lymphoma. H. pylori reside within the gastric mucus layer, mainly composed of mucins carrying an array of glycan structures that can serve as bacterial adhesion epitopes. The aim of the present study was to characterize the binding ability, adhesion modes, and growth of H. pylori strains from pediatric patients with NUD and PUD to gastric mucins. Our results showed an increased adhesion capacity of pediatric PUD H. pylori strains to human and rhesus monkey gastric mucins compared to the NUD strains both at neutral and acidic pH, regardless if the mucins were positive for Lewis b (Leb), Sialyl-Lewis x (SLex) or LacdiNAc. In addition to babA positive strains being more common among PUD associated strains, H. pylori babA positive strains bound more avidly to gastric mucins than NUD babA positive strains at acidic pH. Binding to Leb was higher among babA positive PUD H. pylori strains compared to NUD strains at neutral, but not acidic, pH. PUD derived babA-knockout mutants had attenuated binding to mucins and Leb at acidic and neutral pH, and to SLex and DNA at acidic pH. The results highlight the role of BabA-mediated adherence of pediatric ulcerogenic H. pylori strains, and points to a role for BabA in adhesion to charged structures at acidic pH, separate from its specific blood group binding activity.
Characterization of DNA double‐strand break repair pathways in diffuse large B cell lymphoma

Efficient DNA repair is indispensable for maintaining genomic integrity in humans. Cancer associated deletions and mutations are mainly due to misrepaired DNA double‐strand breaks (DSBs). Classical nonhomologous end joining (c‐NHEJ) and homologous recombination (HR) are two major DSB repair pathways in humans. An error prone, alternative NHEJ pathway that utilizes microhomology was also reported in cancer cells and to a lesser extent in normal cells. In the present study, we evaluated the efficiency of various DSB repair pathways in the most common lymphoma, the diffuse large B cell lymphoma (DLBCL). Here we show that DNA repair through c‐NHEJ pathway is limited in SUDHL8, a cell line derived from a DLBCL patient. Unlike c‐NHEJ, microhomology mediated end joining (MMEJ) was predominant at physiological temperature. Consistent with the observation, expression level of repair proteins such as LIGASE I, LIGASE III, PARP1, CtIP, and MRE11 was higher in DLBCL cells when compared to c‐NHEJ proteins. Further, inhibition of LIGASE I or MRE11, led to reduction in the efficiency of MMEJ in DLBCL cells. Besides, HR‐mediated DSB repair occurring through gene conversion was observed. Thus, our results reveal the predominance of MMEJ over c‐NHEJ in repairing DSBs in DLBCL cells, while error‐free repair through HR was also evident.
Real-Time Workload Classification during Driving using HyperNetworks

Classifying human cognitive states from behavioral and physiological signals is a challenging problem with important applications in robotics. The problem is challenging due to the data variability among individual users, and sensor artefacts. In this work, we propose an end-to-end framework for real-time cognitive workload classification with mixture Hyper Long Short Term Memory Networks (m-HyperLSTM), a novel variant of HyperNetworks. Evaluating the proposed approach on an eye-gaze pattern dataset collected from simulated driving scenarios of different cognitive demands, we show that the proposed framework outperforms previous baseline methods and achieves 83.9% precision and 87.8% recall during test. We also demonstrate the merit of our proposed architecture by showing improved performance over other LSTM-based methods.
Change in quality of life in relation to returning to work after acquired brain injury: a population-based register study

ABSTRACT Purpose: This study investigated changes in quality of life (QoL) in relation to return to work among patients with acquired brain injury (ABI). Method: The sample consisted of 1487 patients with ABI (63% men) aged 18–66 years (mean age 52) from the WebRehab Sweden national quality register database. Only patients who worked at least 50% at admission to hospital and were on full sick leave at discharge from hospital were included. QoL was measured by the EuroQol EQ-5D questionnaire. Results: Patients who returned to work perceived a larger improvement in QoL from discharge to follow-up one year after injury compared to patients who had not returned to work. This difference remained after adjustment for other factors associated with improved QoL, such as having a university education, increased Extended Glasgow Outcome Scale scores and getting one’s driving licence reinstated. Conclusion: Return to work is an important factor for change in QoL among patients with ABI, even after adjusting for other factors related to QoL. This is consistent with the hypothesis that having employment is meaningful, increases self-esteem and fosters participation in society. Thus, helping patients with ABI return to work has a positive influence on QoL.
Root Microbiota in Primary and Secondary Apical Periodontitis

Apical periodontitis is an inflammatory disease of the dental periradicular tissues triggered by bacteria colonizing necrotic root canals. Primary apical periodontitis results from the microbial colonization of necrotic pulp tissues. Secondary apical periodontitis results from a persistent infection of incorrectly treated root canals. The aim of this study was to characterize the microbiota present in primary and secondary intraradicular infections associated with apical periodontitis using 16S rRNA gene amplicon sequencing. Teeth exhibiting apical periodontitis with or without root canal treatment were extracted after informed consent. From each tooth, the intraradicular content as well as a dentin sample (control) were collected and subjected to DNA extraction. PCR amplicons of the V3–V4 region of the bacterial 16S rRNA gene were pooled and sequenced (2 × 300) on an Illumina MiSeq instrument. The bioinformatics analysis pipeline included quality filtering, merging of forward and reverse reads, clustering of reads into operational taxonomic units (OTUs), removal of putative contaminant OTUs and assigning taxonomy. The most prevalent and abundant OTU in both dentin and root canal samples was assigned to anaerobic bacterium Fusobacterium nucleatum. Multivariate analysis showed clustering of microbiota by sample type (dentin vs. intraradicular content) and, in root canals, by pathology (primary vs. secondary infection). The proportions of Enterococcus faecalis and F. nucleatum were, respectively, higher and lower when comparing secondary to primary infected root canals. Co-occurrence network analysis provided evidence of microbial interactions specific to the infection type. The identification of bacterial taxa differentially abundant in primary and secondary intraradicular infections may provide the basis for targeted therapeutic approaches aimed at reducing the incidence of apical periodontitis.
Potent neutralizing antibodies in humans infected with zoonotic simian foamy viruses target conserved epitopes located in the dimorphic domain of the surface envelope protein

Human diseases of zoonotic origin are a major public health problem. Simian foamy viruses (SFVs) are complex retroviruses which are currently spilling over to humans. Replication-competent SFVs persist over the lifetime of their human hosts, without spreading to secondary hosts, suggesting the presence of efficient immune control. Accordingly, we aimed to perform an in-depth characterization of neutralizing antibodies raised by humans infected with a zoonotic SFV. We quantified the neutralizing capacity of plasma samples from 58 SFV-infected hunters against primary zoonotic gorilla and chimpanzee SFV strains, and laboratory-adapted chimpanzee SFV. The genotype of the strain infecting each hunter was identified by direct sequencing of the env gene amplified from the buffy coat with genotype-specific primers. Foamy virus vector particles (FVV) enveloped by wild-type and chimeric gorilla SFV were used to map the envelope region targeted by antibodies. Here, we showed high titers of neutralizing antibodies in the plasma of most SFV-infected individuals. Neutralizing antibodies target the dimorphic portion of the envelope protein surface domain. Epitopes recognized by neutralizing antibodies have been conserved during the cospeciation of SFV with their nonhuman primate host. Greater neutralization breadth in plasma samples of SFV-infected humans was statistically associated with smaller SFV-related hematological changes. The neutralization patterns provide evidence for persistent expression of viral proteins and a high prevalence of coinfection. In conclusion, neutralizing antibodies raised against zoonotic SFV target immunodominant and conserved epitopes located in the receptor binding domain. These properties support their potential role in restricting the spread of SFV in the human population.
In‐vitro analysis of a novel ‘add‐on’ silicone cuff to improve sealing properties of tracheal tubes

Leakage of colonised oropharyngeal secretions across the tracheal tube cuff may cause iatrogenic pulmonary infection. We studied a novel ‘add‐on’ cuff, which can be inserted over an existing tracheal tube and advanced into the subglottic region. The physical properties of the novel silicone cuff (BronchoGuard, Ciel Medical, USA) were evaluated in comparison with the Hi‐Lo® tracheal tube. In a bench study, we identified saline inflation volumes required to transmit pressures between 15 and 30 cmH2O against artificial tracheas of 18, 20 and 22 mm internal diameter. We computed cuff compliance, and minimal inflation volume to achieve air sealing during mechanical ventilation. Finally, we compared the leakage flow rate of artificial saliva across the novel cuff. On average, the mean (SD) inflation volumes necessary to transmit tracheal pressures of 15, 20, 25 and 30 cmH2O were 4.1 (2.2), 4.4 (2.3), 4.6 (2.4) and 4.8 (2.4) ml for the novel cuff and 7.7 (2.5), 8.0 (2.6), 8.4 (2.6) and 8.7 (2.7) ml for the Hi‐Lo tube, respectively (p < 0.001). The minimal inflation volumes to achieve air sealing were 3.8 (0.9) and 10.5 (2.1) ml (p < 0.001), which resulted in transmitted tracheal pressures of 8.3 (9.8) and 27.6 (34.8) cmH2O (p < 0.001). Compliance was 0.026 (0.004) and 0.616 (0.324) ml.cmH20−1, respectively (p < 0.001). Although massive leak was found when the novel cuff transmitted pressures ≤ 20 cmH2O against the trachea, leakage was avoided with pressures ≥ 25 cmH2O, owing to optimal contact between the cuff and the tracheal wall. In contrast, the standard cuff consistently leaked irrespective of the pressure. We conclude that the novel cuff has advantageous properties that warrant clinical corroboration.
Widespread reduction in sun-induced fluorescence from the Amazon during the 2015/2016 El Niño

The tropical carbon balance dominates year-to-year variations in the CO2 exchange with the atmosphere through photosynthesis, respiration and fires. Because of its high correlation with gross primary productivity (GPP), observations of sun-induced fluorescence (SIF) are of great interest. We developed a new remotely sensed SIF product with improved signal-to-noise in the tropics, and use it here to quantify the impact of the 2015/2016 El Niño Amazon drought. We find that SIF was strongly suppressed over areas with anomalously high temperatures and decreased levels of water in the soil. SIF went below its climatological range starting from the end of the 2015 dry season (October) and returned to normal levels by February 2016 when atmospheric conditions returned to normal, but well before the end of anomalously low precipitation that persisted through June 2016. Impacts were not uniform across the Amazon basin, with the eastern part experiencing much larger (10–15%) SIF reductions than the western part of the basin (2–5%). We estimate the integrated loss of GPP relative to eight previous years to be 0.34–0.48 PgC in the three-month period October–November–December 2015. This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.
Can Auditory Objects Be Subitized?

In vision, humans have the ability to mentally “tag” approximately 4 objects, allowing us to monitor, attend, and interact with them. As a consequence, we can rapidly and accurately enumerate up to 4 objects—a process known as subitizing. Here, we investigate whether a similar ability exists for tagging auditory stimuli and find that only 2 or 3 auditory stimuli can be enumerated with high accuracy. We assess whether this high accuracy indicates the existence of an auditory subitizing mechanism, and if it is influenced by factors known to influence visual subitizing. On the basis of accuracy, Experiments 1 and 2 reveal a potential auditory subitizing mechanism only when stimuli are spatially separated, as is the case for visual subitizing. Experiment 3 failed to show any evidence of auditory subitizing when objects were separated in time, rather than space. All three experiments provide only limited evidence for an age-related decline in auditory enumeration of small numbers of objects. This suggests that poor auditory tagging does not contribute significantly to older adults’ difficulties in multitalker conversations. We hypothesize that although auditory subitizing might occur, it is restricted to approximately 2 spatially separated objects due to the difficulty of parsing the auditory scene into its constituent parts.
Emotion recognition depends on subjective emotional experience and not on facial expressivity: evidence from traumatic brain injury

ABSTRACT Background: Recognizing how others feel is paramount to social situations and commonly disrupted following traumatic brain injury (TBI). This study tested whether problems identifying emotion in others following TBI is related to problems expressing or feeling emotion in oneself, as theoretical models place emotion perception in the context of accurate encoding and/or shared emotional experiences. Methods: Individuals with TBI (n = 27; 20 males) and controls (n = 28; 16 males) were tested on an emotion recognition task, and asked to adopt facial expressions and relay emotional memories according to the presentation of stimuli (word and photos). After each trial, participants were asked to self-report their feelings of happiness, anger and sadness. Judges that were blind to the presentation of stimuli assessed emotional facial expressivity. Results: Emotional experience was a unique predictor of affect recognition across all emotions while facial expressivity did not contribute to any of the regression models. Furthermore, difficulties in recognizing emotion for individuals with TBI were no longer evident after cognitive ability and experience of emotion were entered into the analyses. Conclusions: Emotion perceptual difficulties following TBI may stem from an inability to experience affective states and may tie in with alexythymia in clinical conditions.
Stigma and the in(visible) perspectives and expectations of home oxygen therapy among people with chronic breathlessness syndrome: A qualitative study

Background: Chronic breathlessness syndrome in the context of advancing disease is distressing for all concerned. Oxygen is commonly prescribed in this setting; however, little is known about the perspectives of breathless people who either are on oxygen or are yet to have it prescribed. Aim: To understand and describe the perspectives and experiences of breathless people towards oxygen use at home. Design: This qualitative study utilised an interpretive description approach using semi-structured interviews and thematic analysis. Setting/participants: A total of 19 people with chronic breathlessness syndrome living in South Australia participated in semi-structured interviews. Participants were divided into sub-groups according to whether they were chronically breathless and (1) not using home oxygen (n = 6), (2) using funded home oxygen for severe hypoxaemia (n = 7) and (3) using home oxygen for palliation outside of funding guidelines (n = 6). Results: Three main themes were identified: (1) managing distress and living with chronic breathlessness syndrome, with or without oxygen, requires a range of self-management strategies; (2) expectations of oxygen use: ‘Not as good as I thought it would be’; and (3) the stigma of using oxygen: the visible and invisible. Conclusion: People living with chronic breathlessness struggle daily with both the progression of the underlying disease and the distressing nature of the syndrome. While oxygen does provide benefit for some people, its use and the perceptions of its use are often associated with both the visible and invisible manifestations of stigma. Clinicians need to promote self-management strategies and give careful thought to the prescribing of home oxygen, especially outside the current funding guidelines.
Calf Circumference as a Screening Tool for Cognitive Frailty in Community-Dwelling Older Adults: The Korean Frailty and Aging Cohort Study (KFACS)

The aim of this study was to examine calf circumference in relation to cognitive frailty in community-dwelling older adults. Cross-sectional analysis was performed on the first-year baseline data of 1559 adults aged 70–84 years enrolled in the Korean Frailty and Aging Cohort Study. The final analysis included 1221 adults who were non-dependent in terms of instrumental activities of daily living, who underwent frailty and cognitive function assessments. Physical frailty was defined using the Fried Frailty Index. Cognitive impairment was defined as a score 1.5 standard deviations below the age-, sex- and education-matched norms on any of four cognitive-function tests. The prevalence of cognitive frailty was 2.8% for men and 3.8% for women. After adjusting for potential confounders, in comparison to the “physically robust without cognitive impairment” group, the estimates of increased odds ratios (ORs) for low calf circumference (<32 cm) were much greater in the prefrail with cognitive impairment (OR 4.62, 95% confidence interval (CI): 2.02–10.61) and frail with cognitive impairment (OR 10.94, 95% CI: 2.87–41.68) groups in men but not in women. Low calf circumference was strongly related to cognitive frailty in men only, suggesting calf circumference can be used as an indicator of these outcomes.
Do tall tree species have higher relative stiffness than shorter species?

PREMISE OF THE STUDY In 1757 Leonhard Euler demonstrated that to avoid bending tall columns needed to be stiffer but not stronger than shorter columns of equal diameter and material density. Many researchers have concluded that trees have a fixed stiffness to basic density ratio, and therefore, trees adjust for increasing height by adding mass to adjust stem form. But the wood science literature points to considerable variance in stiffness with respect to green wood density. METHODS Using the vast global repository of green wood mechanical properties, we compared relative stiffness and relative strength between taller and shorter species. For North American trees, we examined stem moisture distribution. KEY RESULTS For all regions of the world, taller species on average possessed greater stiffness, but not strength, than shorter species of equal basic specific gravity. We looked for a possible universal mechanism that might allow taller tree species to adjust stiffness without affecting xylem specific gravity and concluded that the evidence points to a decrease in cellulose microfibril angle in structural cell walls combined with possible increases in holocellulose percentage. The evidence is strongest for conifers. We also showed that tall conifers have the ability to adjust the distribution of xylem moisture to maximize conduction while minimizing column load. CONCLUSIONS Our research reveals that taller trees have developed internal stem adjustments to minimize diameter increase while attaining ever-greater heights, thus enabling these taller species to reduce energy expended on biomass accumulation while gaining greater access to solar radiation.
Model-Based Software Engineering: A Multiple-Case Study on Challenges and Development Efforts

A recurring theme in discussions about the adoption of Model-Based Engineering (MBE) is its effectiveness. This is because there is a lack of empirical assessment of the processes and (tool-)use of MBE in practice. We conducted a multiple-case study by observing 2 two-month MBE projects from which software for a Mars rover were developed. We focused on assessing the distribution of the total software development effort over different development activities. Moreover, we observed and collected challenges reported by the developers during the execution of projects. We found that the majority of the effort is spent on the collaboration and communication activities. Furthermore, our inquiry into challenges showed that tool-related challenges are the most encountered.
Bringing Order to Chaos

This work is dedicated to eliminating the overhead required for guaranteeing the storage order in the modern IO stack. The existing block device adopts a prohibitively expensive approach in ensuring the storage order among write requests: interleaving the write requests with Transfer-and-Flush. For exploiting the cache barrier command for flash storage, we overhaul the IO scheduler, the dispatch module, and the filesystem so that these layers are orchestrated to preserve the ordering condition imposed by the application with which the associated data blocks are made durable. The key ingredients of Barrier-Enabled IO stack are Epoch-based IO scheduling, Order-Preserving Dispatch, and Dual-Mode Journaling. Barrier-enabled IO stack can control the storage order without Transfer-and-Flush overhead. We implement the barrier-enabled IO stack in server as well as in mobile platforms. SQLite performance increases by 270% and 75%, in server and in smartphone, respectively. In a server storage, BarrierFS brings as much as by 43 × and by 73× performance gain in MySQL and SQLite, respectively, against EXT4 via relaxing the durability of a transaction.
Impact of the 2015/2016 El Niño on the terrestrial carbon cycle constrained by bottom-up and top-down approaches

Evaluating the response of the land carbon sink to the anomalies in temperature and drought imposed by El Niño events provides insights into the present-day carbon cycle and its climate-driven variability. It is also a necessary step to build confidence in terrestrial ecosystems models' response to the warming and drying stresses expected in the future over many continents, and particularly in the tropics. Here we present an in-depth analysis of the response of the terrestrial carbon cycle to the 2015/2016 El Niño that imposed extreme warming and dry conditions in the tropics and other sensitive regions. First, we provide a synthesis of the spatio-temporal evolution of anomalies in net land–atmosphere CO2 fluxes estimated by two in situ measurements based on atmospheric inversions and 16 land-surface models (LSMs) from TRENDYv6. Simulated changes in ecosystem productivity, decomposition rates and fire emissions are also investigated. Inversions and LSMs generally agree on the decrease and subsequent recovery of the land sink in response to the onset, peak and demise of El Niño conditions and point to the decreased strength of the land carbon sink: by 0.4–0.7 PgC yr−1 (inversions) and by 1.0 PgC yr−1 (LSMs) during 2015/2016. LSM simulations indicate that a decrease in productivity, rather than increase in respiration, dominated the net biome productivity anomalies in response to ENSO throughout the tropics, mainly associated with prolonged drought conditions. This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.