Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance

Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. ABSTRACT Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST). We set high requirements for discriminatory power by using the slowly evolving bacterium Bordetella pertussis as a model pathogen. Our results show that the increased raw read accuracy enables the description of epidemiological scenarios and phylogenetic linkages at the level of gold-standard short reads. The same was true for our variant analysis of vaccine antigens, resistance genes, and virulence factors, demonstrating that nanopore sequencing is a legitimate competitor in the area of next-generation sequencing (NGS)-based high-resolution bacterial typing. Furthermore, we evaluated the parameters for the fastest possible analysis of the data. By combining the optimized processing pipeline with real-time basecalling, we established a workflow that allows for highly accurate and extremely fast high-resolution typing of bacterial pathogens while sequencing is still in progress. Along with advantages such as low costs and portability, the approach suggested here might democratize modern bacterial typing, enabling more efficient infection control globally.
[Analysis of the pathogenesis and risk factors of gallstone].

Objective: To explore the pathogenesis and risk factors of gallstone formation. Methods: The findings of hepatobiliary ultrasound and related data were collected from healthy subjects who underwent a physical examination at Xuanwu Hospital of Capital Medical University from January 2012 to December 2021. A total of 98 344 healthy subjects were included in the study,including 48 241 males and 50 103 females,with a ratio of 1∶1.03,aged (42.0±15.6)years(range:14 to 97 years). The gender,age,body mass index,waist circumference,systolic pressure,diastolic pressure,ALT,AST,total bilirubin,fasting blood glucose,triglyceride,total cholesterol,low-density lipoprotein,high-density lipoprotein were collected.Healthy subjects were required to sit for at least 10 minutes before blood pressure was measured.Rresults of fasting venous blood were collected after 8 to 12 hours on an empty stomach.According to the presence of gallstones by ultrasound results, healthy subjects were divided into study group and control group. Data were analyzed by rank-sum tests and χ2 test, and risk factors for gallstone formation were explored by Logistic regression analysis. Results: The incidence of gallstones in this group was 5.42%(5 333/98 344). Among them,the incidence of gallstones in people aged 60 years and above was significantly higher than that in people under 60 years old(15.31%(2 348/15 334) vs. 3.60%(2 985/83 010), χ2=3 473.46,P<0.05). The healthy subjects were divided by age for every 10 years,and the results showed that the incidence of gallstones increased with age. The incidence of gallstones in females was 5.68%(2 844/50 103),greater than 5.16%(2 489/48 241) in males(χ2=11.81,P<0.05). Among them,1 478 cases underwent gallbladder surgical resection due to gallstones,and the operation rate was 27.71%. The operation rate reached the peak between 60 and <70 years old,and decreased after 70 years old. The results of the multivariate analysis showed that,female(OR=1.38, P<0.01),age(OR=1.58, P<0.01),body mass index≥24 kg/m2(OR=1.31, P<0.01),waist circumference≥85 cm(OR=1.24, P<0.01),fasting blood glucose>6.1 mmol/L(OR=1.18,P<0.01),total cholesterol≥5.18 mmol/L(OR=0.87, P=0.019),low-density lipoprotein≥3.37 mmol/L(OR=1.15,P=0.001) were the risk factors for gallstone formation;high-density lipoprotein≥1.55 mmol/L(OR=0.87, P<0.01) was a protective factor for gallstone formation. Conclusions: The incidence of gallstones increases with age in male and female. Gender,age,body mass index,waist circumferenc,fasting blood glucose,total cholesterol,LDL,and HDL are related factors with gallstone formation.
Impact of Pneumococcal and Viral Pneumonia on the Respiratory and Intestinal Tract Microbiomes of Mice

Pneumonia is one of the leading causes of death worldwide. Here, we compared the impact of bacterial- and viral-induced pneumonia on the respiratory and gastrointestinal microbiome. Using a meta-omics approach, we identified specific profiles that allow discrimination between bacterial and viral causative. ABSTRACT With 2.56 million deaths worldwide annually, pneumonia is one of the leading causes of death. The most frequent causative pathogens are Streptococcus pneumoniae and influenza A virus. Lately, the interaction between the pathogens, the host, and its microbiome have gained more attention. The microbiome is known to promote the immune response toward pathogens; however, our knowledge on how infections affect the microbiome is still scarce. Here, the impact of colonization and infection with S. pneumoniae and influenza A virus on the structure and function of the respiratory and gastrointestinal microbiomes of mice was investigated. Using a meta-omics approach, we identified specific differences between the bacterial and viral infection. Pneumococcal colonization had minor effects on the taxonomic composition of the respiratory microbiome, while acute infections caused decreased microbial complexity. In contrast, richness was unaffected following H1N1 infection. Within the gastrointestinal microbiome, we found exclusive changes in structure and function, depending on the pathogen. While pneumococcal colonization had no effects on taxonomic composition of the gastrointestinal microbiome, increased abundance of Akkermansiaceae and Spirochaetaceae as well as decreased amounts of Clostridiaceae were exclusively found during invasive S. pneumoniae infection. The presence of Staphylococcaceae was specific for viral pneumonia. Investigation of the intestinal microbiomés functional composition revealed reduced expression of flagellin and rubrerythrin and increased levels of ATPase during pneumococcal infection, while increased amounts of acetyl coenzyme A (acetyl-CoA) acetyltransferase and enoyl-CoA transferase were unique after H1N1 infection. In conclusion, identification of specific taxonomic and functional profiles of the respiratory and gastrointestinal microbiome allowed the discrimination between bacterial and viral pneumonia. IMPORTANCE Pneumonia is one of the leading causes of death worldwide. Here, we compared the impact of bacterial- and viral-induced pneumonia on the respiratory and gastrointestinal microbiome. Using a meta-omics approach, we identified specific profiles that allow discrimination between bacterial and viral causative.
Similarity to the self influences memory for social targets

ABSTRACT The construct of the self is important in the domain of memory research. Recent work has shown that person memory is influenced by similarity of social targets to the self. The current experiments investigate self-similarity as defined by traits and political ideology to better understand how memory for social targets is organised. Across three experiments, participants formed positive or negative impressions based on each target’s picture, a trait-implying behavior (Experiments 1 & 2), and/or political ideology (conservative/liberal label in Experiment 2; political-ideological belief statements in Experiment 3) followed by a memory test. Results showed a self-similarity effect dependent on valence in Experiment 1, but not in Experiments 2 or 3 when participants processed ideological information associated with targets. These results suggest that self-similarity has an effect on memory for social targets, but that ideological information disrupts self-focused processing of others, suggesting that ideological information also has a powerful influence on what people remember about others (i.e. social targets).
Diverticulosis is not associated with altered gut microbiota nor is it predictive of future diverticulitis: a population-based colonoscopy study

Abstract Background The etiopathogenesis of diverticular disease is unknown. Objective To compare the fecal and mucosa-associated microbiota between participants with and without diverticulosis and participants who later developed diverticulitis versus those that did not from a population-based study. Methods The PopCol study, conducted in Stockholm, Sweden, invited a random sample of 3556 adults to participate, of which 745 underwent colonoscopy. Overall, 130 participants (17.5%) had diverticulosis. 16S rRNA gene sequencing was conducted on available sigmoid biopsy samples from 529 and fecal samples from 251 individuals. We identified individuals who subsequently developed acute diverticulitis up to 13 years after sample collection. In a case-control design matching for gender, age (+/−5 years), smoking and antibiotic exposure, we compared taxonomic composition, richness and diversity of the microbiota between participants with or without diverticulosis, and between participants who later developed acute diverticulitis versus those who did not. Results No differences in microbiota richness or diversity were observed between participants with or without diverticulosis, nor for those who developed diverticulitis compared with those who did not. No bacterial taxa were significantly different between participants with diverticulosis compared with those without diverticulosis. Individuals who later developed acute diverticulitis (2.8%) had a higher abundance of genus Comamonas than those who did not (p = .027). Conclusions In a population-based cohort study the only significant difference was that those who later develop diverticulitis had more abundance of genus Comamonas. The significance of Comamonas is unclear, suggesting a limited role for the gut microbiota in the etiopathogenesis of diverticular disease.
Length Matters: Informational Load in Ambiguity Resolution

In this paper, we will compare prosodic and pragmatic approaches to the role of constituent length in attachment ambiguities. Lengthening a constituent affects its informativity: longer constituents are usually less predictable (Levy & Florian, 2007) and demand a higher processing load than shorter ones (Almor, 1999). Following neo-Gricean accounts (Levinson, 1987 and 1991), increased informational load needs to be justified. This justification is achieved more easily when the long constituent conveys new information and when it relates to central elements of the utterance. Informational load is, however, not a simple question of length in numbers of characters or syllables but more likely a question of amount of information. In three off-line experiments using a cloze task, we will compare the effect of lengthening ambiguous prepositional phrases as in [1a/b/c] either by lengthening a city name or by adding information about the city. We will show that only lengthening by adding information increases attachment to a more central element of the utterance. These results will be discussed based on prosodic and pragmatic factors explaining the role of constituent length for attachment ambiguities. [1] Peter met the doctor of the lawyer from a. Apt. / b. Aix-en-Provence / c. the beautiful city of Apt.
Ultrasound-guided Techniques for Perioperative Analgesia in Pediatric Lower Abdominal Surgeries: Quadratus Lumborum Block with Bupivacaine versus Caudal Bupivacaine and Neostigmine.

BACKGROUND Ultrasound-guided regional anesthesia techniques for perioperative analgesia in pediatric patients scheduled for lower abdominal surgeries can be achieved either by quadratus lumborum block (QLB) or caudal block (CB). Neostigmine was co-administered with caudal bupivacaine to shorten the onset and extend the duration of analgesia. OBJECTIVES This study aimed to compare between 2 ultrasound-guided techniques used for perioperative analgesia (QLB with bupivacaine vs. CB with bupivacaine/neostigmine) regarding the total amount of rescue analgesic (acetaminophen mg/kg) used for pain relief at 24 hours postsurgery in pediatric patients undergoing lower abdominal surgeries in a developing country and to discuss existing barriers during the implementation of both techniques. STUDY DESIGN A randomized, double-blind, prospective, single-center study. SETTING Ain-Shams University Hospitals. METHODS Eighty pediatric patients scheduled for lower abdominal surgeries under general anesthesia were randomly allocated to receive either ultrasound-guided QLB using bupivacaine or ultrasound-guided CB using a bupivacaine/neostigmine mixture. The total amount of rescue analgesic (acetaminophen mg/kg) 24 hours postsurgery was considered as the primary outcome while the time to first rescue analgesia, pain score, postoperative nausea and vomiting, bradycardia, hypotension, and urinary retention were considered as secondary outcomes. RESULTS In the QLB group, the time to first rescue analgesia was longer whereas the total analgesic dose (mg/kg) was lower than the CB group (P < 0.001, P = 0.007, respectively). While, on the other hand, in CB group, the time to perform the block was shorter and Parents Satisfaction Score 24 h postsurgery was lower than the QLB group (P < 0.001, P < 0.001, respectively). Side effects were infrequent and comparable between the study groups. LIMITATIONS First, the researchers did not assess the dermatomal level before or after the operation in either group. Second, the investigators should have noticed the first voiding time to demonstrate accurately the incidence of urine retention. Third, a cost-effectiveness analysis of perioperative costs (drugs, staff, resources being used) of these regional anesthesia techniques when applied in an ambulatory setting should have been done, which would be helpful for those in resource-limited settings. CONCLUSIONS Postoperative analgesia for pediatric patients undergoing lower abdominal surgeries can be safely and effectively achieved by QLB with bupivacaine and a CB with a bupivacaine/neostigmine mixture with priority given to CB, especially in resource-limited settings.
2-Oxidation, 3-methyl hydroxylation, and 6-hydroxylation of skatole, a contributor to the odour of boar-tainted pork meat, mediated by porcine liver microsomal cytochromes P450 1A2, 2A19, 2E1, and 3A22

Abstract The 2-oxidation, 3-methyl hydroxylation, and 6-hydroxylation of skatole (a contributor to boar taint) mediated by minipig liver microsomes and recombinant P450 enzymes expressed in bacterial membranes were investigated. At low substrate concentrations of 10 µM, the formation rates of indole-3-carbinol, 6-hydroxyskatole, and the sum of 3-methyloxindole, indole-3-carbinol, and 6-hydroxyskatole in male minipig liver microsomes were significantly lower than those in female minipig liver microsomes. Compensatory 3-methyloxindole and indole-3-carbinol formation in minipig liver microsomes, which lack 6-hydroxyskatole formation in males, was mediated partly by liver microsomal P450 1A2 and P450 1A2/2E1, respectively. These enzymes were suppressed by typical P450 inhibitors in female minipig liver microsomes. Among the 14 pig P450 forms evaluated, P450 2A19 was the dominant form mediating 3-methyloxindole, indole-3-carbinol, and 6-hydroxyskatole formation from skatole at substrate concentrations of 100 µM. Positive cooperativity was observed in 3-methyloxindole formation from skatole mediated by male minipig liver microsomes and by pig P450 3A22 with Hill coefficients of 1.2–1.5. These results suggest high skatole 2-oxidation, 3-methyl hydroxylation, and 6-hydroxylation activities of pig P450 2A19 and compensatory skatole oxidations mediated by pig P450 1A2, 2E1, or 3A22 in male minipig liver microsomes.
Splenic flexure cancer survival: a 25‐year experience and implications for complete mesocolic excision (CME) and central vascular ligation (CVL)

The management of splenic flexure cancers (SFCs) in the era of complete mesocolic excision (CME) and central vascular ligation (CVL) is challenging because of its variable lymphatic drainage. This study aimed to compare survival outcomes for SFCs and non‐SFCs, and better understand the clinicopathological characteristics which may define a distinct SFC phenotype.
Systematic Human Learning and Generalization From a Brief Tutorial With Explanatory Feedback

Abstract We investigate human adults’ ability to learn an abstract reasoning task quickly and to generalize outside of the range of training examples. Using a task based on a solution strategy in Sudoku, we provide Sudoku-naive participants with a brief instructional tutorial with explanatory feedback using a narrow range of training examples. We find that most participants who master the task do so within 10 practice trials and generalize well to puzzles outside of the training range. We also find that most of those who master the task can describe a valid solution strategy, and such participants perform better on transfer puzzles than those whose strategy descriptions are vague or incomplete. Interestingly, fewer than half of our human participants were successful in acquiring a valid solution strategy, and this ability was associated with completion of high school algebra and geometry. We consider the implications of these findings for understanding human systematic reasoning, as well as the challenges these findings pose for building computational models that capture all aspects of our findings, and we point toward a role for learning from instructions and explanations to support rapid learning and generalization.
Operational Neural Networks for Parameter-Efficient Hyperspectral Single-Image Super-Resolution

Hyperspectral imaging is a crucial tool in remote sensing, which captures far more spectral information than standard color images. However, the increase in spectral information comes at the cost of spatial resolution. Super-resolution is a popular technique where the goal is to generate a high-resolution version of a given low-resolution input. The majority of modern super-resolution approaches use convolutional neural networks (CNNs). However, convolution itself is a linear operation and the networks rely on the nonlinear activation functions after each layer to provide the necessary nonlinearity to learn the complex underlying function. This means that CNNs tend to be very deep to achieve the desired results. Recently, self-organized operational neural networks (ONNs) have been proposed that aim to overcome this limitation by replacing the convolutional filters with learnable nonlinear functions through the use of MacLaurin series expansions. This work focuses on extending the convolutional filters of a popular super-resolution model to more powerful operational filters to enhance the model performance on hyperspectral images (HSIs). We also investigate the effects that residual connections and different normalization types have on this type of enhanced network. Despite having fewer parameters than their convolutional network equivalents, our results show that ONNs achieve superior super-resolution performance on small HSI datasets.
EMRI + TDE = QPE: Periodic X-Ray Flares from Star–Disk Collisions in Galactic Nuclei

Roughly half of the quasiperiodic eruption (QPE) sources in galactic nuclei exhibit a remarkably regular alternating “long-short” pattern of recurrence times between consecutive flares. We show that a main-sequence star (brought into the nucleus as an extreme mass-ratio inspiral; EMRI) that passes twice per orbit through the accretion disk of the supermassive black hole (SMBH) on a mildly eccentric inclined orbit, each time shocking and ejecting optically thick gas clouds above and below the midplane, naturally reproduces observed properties of QPE flares. Inefficient photon production in the ejecta renders the QPE emission much harder than the blackbody temperature, enabling the flares to stick out from the softer quiescent disk spectrum. Destruction of the star via mass ablation limits the QPE lifetime to decades, precluding a long-lived AGN as the gaseous disk. By contrast, a tidal disruption event (TDE) naturally provides a transient gaseous disk on the requisite radial scale, with a rate exceeding the EMRI inward migration rate, suggesting that many TDEs should host a QPE. This picture is consistent with the X-ray TDE observed several years prior to the QPE appearance from GSN 069. Remarkably, a second TDE-like flare was observed from this event, starting immediately after detectable QPE activity ceased; this event could plausibly result from the (partial or complete) destruction of the QPE-generating star triggered by runaway mass loss, though other explanations cannot be excluded. Our model can also be applied to black hole–disk collisions, such as those invoked in the context of the candidate SMBH binary OJ 287.
Infeasible Deterministic, Stochastic, and Variance-Reduction Algorithms for Optimization under Orthogonality Constraints

Orthogonality constraints naturally appear in many machine learning problems, from Principal Components Analysis to robust neural network training. They are usually solved using Riemannian optimization algorithms, which minimize the objective function while enforcing the constraint. However, enforcing the orthogonality constraint can be the most time-consuming operation in such algorithms. Recently, Ablin&Peyr\'e (2022) proposed the Landing algorithm, a method with cheap iterations that does not enforce the orthogonality constraint but is attracted towards the manifold in a smooth manner. In this article, we provide new practical and theoretical developments for the landing algorithm. First, the method is extended to the Stiefel manifold, the set of rectangular orthogonal matrices. We also consider stochastic and variance reduction algorithms when the cost function is an average of many functions. We demonstrate that all these methods have the same rate of convergence as their Riemannian counterparts that exactly enforce the constraint. Finally, our experiments demonstrate the promise of our approach to an array of machine-learning problems that involve orthogonality constraints.
Simplification and Improvement of MMS Approximation

We consider the problem of fairly allocating a set of indivisible goods among n agents with additive valuations, using the popular fairness notion of maximin share (MMS). Since MMS allocations do not always exist, a series of works provided existence and algorithms for approximate MMS allocations. The Garg-Taki algorithm gives the current best approximation factor of (3/4 + 1/12n). Most of these results are based on complicated analyses, especially those providing better than 2/3 factor. Moreover, since no tight example is known of the Garg-Taki algorithm, it is unclear if this is the best factor of this approach. In this paper, we significantly simplify the analysis of this algorithm and also improve the existence guarantee to a factor of (3/4 + min(1/36, 3/(16n-4))). For small n, this provides a noticeable improvement. Furthermore, we present a tight example of this algorithm, showing that this may be the best factor one can hope for with the current techniques.