Miracle-dz/UniFAR-FTUs huggingface dataset:
Coordinated transcriptional response to environmental stress by a Synechococcus virus

Abstract Viruses are a major control on populations of microbes. Often, their virulence is examined in controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in host physiology and fitness that may impart both costs and benefits on viral success. Phosphorus (P) is a major abiotic control on the marine cyanobacterium Synechococcus. Some viruses infecting Synechococcus have acquired, from their host, a gene encoding a P substrate binding protein (PstS), thought to improve virus replication under phosphate starvation. Yet, pstS is uncommon among cyanobacterial viruses. Thus, we asked how infections with viruses lacking PstS are affected by P scarcity. We show that the production of infectious virus particles of such viruses is reduced in low P conditions. However, this reduction in progeny is not caused by impaired phage genome replication, thought to be a major sink for cellular phosphate. Instead, transcriptomic analysis showed that under low P conditions, a PstS-lacking cyanophage increased the expression of a specific gene set that included mazG, hli2, and gp43 encoding a pyrophosphatase, a high-light inducible protein and DNA polymerase, respectively. Moreover, several of the upregulated genes were controlled by the host’s phoBR two-component system. We hypothesize that recycling and polymerization of nucleotides liberates free phosphate and thus allows viral morphogenesis, albeit at lower rates than when phosphate is replete or when phages encode pstS. Altogether, our data show how phage genomes, lacking obvious P-stress–related genes, have evolved to exploit their host’s environmental sensing mechanisms to coordinate their own gene expression in response to resource limitation.
Evaluation of Pre-Chlorinated Wastewater Effluent for Microalgal Cultivation and Biodiesel Production

Microalgae are promising feedstock to produce biodiesel and other value added products. However, the water footprint for producing microalgal biodiesel is enormous and would put a strain on the water resources of water stressed countries like South Africa if freshwater is used without recycling. This study evaluates the utilization of pre-chlorinated wastewater as a cheap growth media for microalgal biomass propagation with the aim of producing biodiesel whilst simultaneously remediating the wastewater. Wastewater was collected from two wastewater treatment plants (WWTPs) in Durban, inoculated with Neochloris aquatica and Asterarcys quadricellulare and the growth kinetics monitored for a period of 8 days. The physicochemical parameters; including chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) were determined before microalgal cultivation and after harvesting. Total lipids were quantified gravimetrically after extraction by hexane/isopropanol (3:2 v/v). Biodiesel was produced by transesterification and characterised by gas chromatography. The total carbohydrate was extracted by acid hydrolysis and quantified by spectrophotometric method based on aldehyde functional group derivatization. Asterarcys quadricellulare utilized the wastewater for growth and reduced the COD of the wastewater effluent from the Umbilo WWTP by 12.4%. Total nitrogen (TN) and phosphorus (TP) were reduced by 48% and 50% respectively by Asterarcys quadricellulare cultivated in sterile wastewater while, Neochloris reduced the TP by 37% and TN by 29%. Although the highest biomass yield (460 mg dry weight) was obtained for Asterarcys, the highest amount of lipid (14.85 ± 1.63 mg L−1) and carbohydrate (14.84 ± 0.1 mg L−1) content were recorded in Neochloris aquatica. The dominant fatty acids in the microalgae were palmitic acid (C16:0), stearic acid (C18:0) and oleic acid (C18:1). The biodiesel produced was determined to be of good quality with high oxidation stability and low viscosity, and conformed to the American society for testing and materials (ASTM) guidelines.
TET1 inhibits the migration and invasion of cervical cancer cells by regulating autophagy

ABSTRACT Methylation modifications play pertinent roles in regulating gene expression and various biological processes. The silencing of the demethylase enzyme TET1 can affect the expressions of key oncogenes or tumour suppressor genes, thus contributing to tumour formation. Nonetheless, how TET1 affects the progression of cervical cancer is yet to be elucidated. In this study, we found that the expression of TET1 was significantly downregulated in cervical cancer tissues. Functionally, TET1 knockdown in cervical cancer cells can promote cell proliferation, migration, invasion, cervical xenograft tumour formation and EMT. On the contrary, its overexpression can reverse the aforementioned processes. Moreover, the autophagy level of cervical cancer cells can be enhanced after TET1 knockdown. Mechanistically, methylated DNA immunoprecipitation (MeDIP)-sequencing and MeDIP quantitative real-time PCR revealed that TET1 mediates the methylation of autophagy promoter regions. These findings suggest that TET1 affects the autophagy of cervical cancer cells by altering the methylation levels of NKRF or HIST1H2AK, but the specific mechanism needs to be investigated further.
Serotonergic neurotransmission mediated cognitive dysfunction in two mouse models of sepsis‐associated encephalopathy

Abstract Background Patients with sepsis‐associated encephalopathy (SAE) often exhibit cognitive impairments. Despite this, the underlying mechanisms of SAE remain largely unexplored. Here, we explored the role of serotonergic neurotransmission in cognitive dysfunction of two mouse models of SAE. Methods The mouse models of SAE were established by injection of lipopolysaccharide (LPS, 10 mg/kg, intraperitoneal) and cecal ligation puncture (CLP) respectively. Barnes maze, new object recognition test and open field test were used to evaluate the effects of fluoxetine (selective serotonin reuptake inhibitor) and cyproheptadine (nonselective 5‐HT2 receptor antagonist) on cognition and motor activity of mice. Additionally, WAY100635 (5‐HT1A receptor antagonist) was co‐administered with fluoxetine to explore the mechanism underlying effect of fluoxetine on cognitive impairments of SAE. Enzyme‐linked immunosorbent assay (ELISA) was performed to determine 5‐HT levels in hippocampus, brainstem and frontal lobe of experimental groups. Results Both LPS‐induced sepsis and CLP induced sepsis resulted in a notable learning deficit. Fluoxetine ameliorated, while cyproheptadine aggravated, cognitive impairment in two classic mouse models of SAE. The cognition‐enhancing effect of fluoxetine is reversed by WAY100635. Decreased 5‐HT levels in hippocampus, brainstem and frontal lobe were observed in LPS septic model and CLP septic model. Notably, both fluoxetine and cyproheptadine significantly increased 5‐HT levels in those brain regions in LPS septic model. Additionally, fluoxetine significantly increased 5‐HT levels in frontal lobe of CLP septic model. Conclusions Our study demonstrated that serotonergic neurotransmission plays a significant role in mechanisms underlying cognitive impairment in SAE. These findings contribute to identification of novel targets to prevent and arrest cognitive impairment in SAE.
A systematic review and meta-analysis

Background: Human cytochrome P450 (CYP) is an enzyme responsible for the metabolic activation of many carcinogens, including nitrosamines. CYP2E1 represents a major CYP isoform and is expressed in the human urothelial cells. Recent studies have investigated the association of CYP2E1 gene polymorphisms with bladder cancer risk but have shown contradictory results. Hence, we performed a systematic literature review andmeta-analysis to assess the association betweenCYP2E1 gene polymorphisms and bladder cancer. Methods:Systematic literature searches were conducted with PubMed, Excerpt Medica Database, Science Direct/Elsevier, China National Knowledge Infrastructure, and the Cochrane Library up to January 2018 for studies that involved the association ofCYP2E1 gene polymorphisms with bladder cancer risk. A meta-analysis was performed with Review Manager and Stata software. Combined odds ratios (ORs) were identified with 95% confidence intervals (CIs) in a random or fixed effects model. Ethics:The protocol was approved by the institutional review board of each study center. Written informed consent will be obtained from all patients before registration, in accordance with the Declaration of Helsinki. Results:Eight studies were identified, including 1733 cases of bladder cancer and 1814 normal controls. Our results illustrated that there are significant associations between CYP2E1 gene polymorphisms and bladder cancer in all genetic models (P< .05). The combined ORs and 95% CIs were as follows for each model: additive model [OR 0.56; 95% CI (0.38–0.82)]; dominant model [OR 0.79; 95% CI (0.67–0.93)]; recessive model [OR 0.61; 95% CI (0.41–0.89)]; codominant model [OR 0.80; 95% CI (0.67–0.96)]; allele model [OR 0.75; 95% CI (0.59–0.95)]. A subgroup study showed that there are also significant associations between CYP2E1 gene polymorphisms and bladder cancer in Asian people. However, there are no significant associations between CYP2E1 gene polymorphisms and bladder cancer in Caucasian populations. Conclusions:The present study provides evidence for an association betweenCYP2E1 gene polymorphisms and bladder cancer progression, and suggests that CYP2E1 gene polymorphisms might be a protective factor against bladder cancer in Asian people. However, studies with larger sample sizes are needed to confirm the correlation between CYP2E1 gene polymorphisms and bladder cancer. Abbreviations: CI = confidence interval, CYP = cytochrome P450, OR = odds ratio, SNP = single nucleotide polymorphism.
Supported decision‐making interventions in mental healthcare: A systematic review of current evidence and implementation barriers

Abstract Background There is a growing momentum around the world to foster greater opportunities for the involvement of mental health service users in their care and treatment planning. In‐principle support for this aim is widespread across mental healthcare professionals. Yet, progress in mental health services towards this objective has lagged in practice. Objectives We conducted a systematic review of quantitative, qualitative and mixed‐method research on interventions to improve opportunities for the involvement of mental healthcare service users in treatment planning, to understand the current research evidence and the barriers to implementation. Methods Seven databases were searched and 5137 articles were screened. Articles were included if they reported on an intervention for adult service users, were published between 2008 and October 2023 and were in English. Evidence in the 140 included articles was synthesised according to the JBI guidance on Mixed Methods Systematic Reviews. Results Research in this field remains exploratory in nature, with a wide range of interventions investigated to date but little experimental replication. Overarching barriers to shared and supported decision‐making in mental health treatment planning were (1) Organisational (resource limitations, culture barriers, risk management priorities and structure); (2) Process (lack of knowledge, time constraints, health‐related concerns, problems completing and using plans); and (3) Relationship barriers (fear and distrust for both service users and clinicians). Conclusions On the basis of the barriers identified, recommendations are made to enable the implementation of new policies and programs, the designing of new tools and for clinicians seeking to practice shared and supported decision‐making in the healthcare they offer. Patient or Public Contribution This systematic review has been guided at all stages by a researcher with experience of mental health service use, who does not wish to be identified at this point in time. The findings may inform organisations, researchers and practitioners on implementing supported decision‐making, for the greater involvement of people with mental ill health in their healthcare.
Cognitive Effects of Toxoplasma and CMV Infections: A Cross-Sectional Study of 557 Young Adults Considering Modulation by Sex and Rh Factor

One-third of humanity harbors a lifelong infection with Toxoplasma gondii. This parasite undergoes sexual reproduction in cats and asexual reproduction in any warm-blooded intermediate hosts. The cycle progresses as cats ingest these hosts, containing the parasite's tissue cysts. Such infections can alter behaviors in both animals and humans, potentially increasing predation risk by felines - usually seen as parasite-induced manipulations. This study aims to delineate toxoplasmosis's effects on cognitive abilities and compare these to the effects of human cytomegalovirus (CMV), which also infects the brain but is not spread through predation. We evaluated the cognitive performance of 557 students, who had been examined for Toxoplasma and CMV infections, using intelligence, memory, and psychomotor tests. Results indicated cognitive impairments in seropositive individuals for both pathogens, with variations in cognitive impact related to sex and Rh factor. Specifically, Toxoplasma was associated with lower IQ in men, whereas CMV predominantly with worse women's memory and reaction speeds. Analysis of antibody concentrations hinted that certain Toxoplasma-associated cognitive detriments may wane (impaired intelligence) or worsen (impaired reaction times) over time following infection. The findings imply that cognitive impairments from both neurotropic pathogens are likely due to pathological changes in the brain rather than direct manipulative actions by the parasites.
RACIAL AND ETHNIC DIFFERENCES IN LONG-TERM CARDIOVASCULAR MORTALITY AMONG WOMEN AND MEN FROM THE CAC CONSORTIUM

Background: Despite an increasingly diverse population, knowledge regarding racial and ethnic disparities is limited among women and men undergoing atherosclerotic cardiovascular (ASCVD) screening. Our aim was to compare CV mortality by ASCVD risk and coronary artery calcium (CAC) scores among Black and Hispanic women and men compared to other participants. Design and Methods: From the CAC Consortium, 42,964 participants with self-reported race and ethnicity were followed for a median of 11.7 years. Multivariable Cox proportional hazards regression models were used to estimate CV mortality, with separate analyses by sex. Results: One-third of enrollees were women; 977 self-reported as Black, 1,349 as Hispanic, 1,621 as Asian, and 740 as American Indian/Native Alaskan/Hawaiian or other; the remainder were white. Black women and men had higher ASCVD risk and CAC scores yielding the highest CV mortality compared to other participants. Among Black women and men with a 0 CAC or ASCVD risk score <5%, hazard ratios (HRs) were 6-9-fold higher than that of other women and men. In men with CAC scores [≥]100, Black men (HR: 4.2,p<0.001) had the highest CV mortality compared to all other men. A similar high-risk pattern was noted for Black women with CAC scores [≥]100 (p<0.001), even when adjusting for the ASCVD risk score. Overall, Hispanics had an elevated CV mortality, higher than others but less than that of Black participants. Patterns of intermediate risk were notable for Hispanic men with a CAC score of 0 (HR=3.6, p=0.006) and [≥]100 (HR=2.3, p=0.03). Conclusions: The disproportionately high and excess CV mortality among Black women and men represents significant barriers to reducing the burden of ASCVD through effective screening using ASCVD risk and CAC scores.
Euclidean distance compression via deep random features

Motivated by the problem of compressing point sets into as few bits as possible while maintaining information about approximate distances between points, we construct random nonlinear maps $\varphi_\ell$ that compress point sets in the following way. For a point set $S$, the map $\varphi_\ell:\mathbb{R}^d \to N^{-1/2}\{-1,1\}^N$ has the property that storing $\varphi_\ell(S)$ (a \emph{sketch} of $S$) allows one to report pairwise squared distances between points in $S$ up to some multiplicative $(1\pm \epsilon)$ error with high probability as long as the minimum distance is not too small compared to $\epsilon$. The maps $\varphi_\ell$ are the $\ell$-fold composition of a certain type of random feature mapping. Moreover, we determine how large $N$ needs to be as a function of $\epsilon$ and other parameters of the point set. Compared to existing techniques, our maps offer several advantages. The standard method for compressing point sets by random mappings relies on the Johnson-Lindenstrauss lemma which implies that if a set of $n$ points is mapped by a Gaussian random matrix to $\mathbb{R}^k$ with $k =\Theta(\epsilon^{-2}\log n)$, then pairwise distances between points are preserved up to a multiplicative $(1\pm \epsilon)$ error with high probability. The main advantage of our maps $\varphi_\ell$ over random linear maps is that ours map point sets directly into the discrete cube $N^{-1/2}\{-1,1\}^N$ and so there is no additional step needed to convert the sketch to bits. For some range of parameters, our maps $\varphi_\ell$ produce sketches which require fewer bits of storage space.
On Hoffman polynomials of $\lambda$-doubly stochastic irreducible matrices and commutative association schemes

Let $\Gamma$ denote a finite (strongly) connected regular (di)graph with adjacency matrix $A$. The {\em Hoffman polynomial} $h(t)$ of $\Gamma=\Gamma(A)$ is the unique polynomial of smallest degree satisfying $h(A)=J$, where $J$ denotes the all-ones matrix. Let $X$ denote a nonempty finite set. A nonnegative matrix $B\in{\mbox{Mat}}_X({\mathbb R})$ is called {\em $\lambda$-doubly stochastic} if $\sum_{z\in X} (B)_{yz}=\sum_{z\in X} (B)_{zy}=\lambda$ for each $y\in X$. In this paper we first show that there exists a polynomial $h(t)$ such that $h(B)=J$ if and only if $B$ is a $\lambda$-doubly stochastic irreducible matrix. This result allows us to define the Hoffman polynomial of a $\lambda$-doubly stochastic irreducible matrix. Now, let $B\in{\mbox{Mat}}_X({\mathbb R})$ denote a normal irreducible nonnegative matrix, and ${\cal B}=\{p(B)\mid p\in{\mathbb{C}}[t]\}$ denote the vector space over ${\mathbb{C}}$ of all polynomials in $B$. Let us define a $01$-matrix $\widehat{A}$ in the following way: $(\widehat{A})_{xy}=1$ if and only if $(B)_{xy}>0$ $(x,y\in X)$. Let $\Gamma=\Gamma(\widehat{A})$ denote a (di)graph with adjacency matrix $\widehat{A}$, diameter $D$, and let $A_D$ denote the distance-$D$ matrix of $\Gamma$. We show that ${\cal B}$ is the Bose--Mesner algebra of a commutative $D$-class association scheme if and only if $B$ is a normal $\lambda$-doubly stochastic matrix with $D+1$ distinct eigenvalues and $A_D$ is a polynomial in $B$.
A Universal Roadmap For Searching Repulsive Casimir Forces Between Magneto-Electric Materials

The Casimir effect, arising from vacuum quantum fluctuations, plays a fundamental role in the development of modern quantum electrodynamics. In parallel, the field of condensed matter has flourished through the discovery of various materials exhibiting broken symmetries, often connected to topology and characterized by magneto-electric coupling. Here, we calculate the Casimir forces between materials with time-reversal symmetry and/or parity symmetry breaking. Remarkably, we obtain a universal phase diagram governing the sign of symmetry-breaking-induced Casimir forces, contributing to a comprehensive understanding on the sign of Casimir force for linear optical materials. The discovered phase diagram serves as a roadmap for searching repulsive Casimir forces, a subject bearing both theoretical interest and practical significance.
Experimental demonstration of scalable cross-entropy benchmarking to detect measurement-induced phase transitions on a superconducting quantum processor

Quantum systems subject to random unitary evolution and measurements at random points in spacetime exhibit entanglement phase transitions which depend on the frequency of these measurements. Past work has experimentally observed entanglement phase transitions on near-term quantum computers, but the characterization approach using entanglement entropy is not scalable due to exponential overhead of quantum state tomography and post selection. Recently, an alternative protocol to detect entanglement phase transitions using linear cross-entropy was proposed which eliminates both bottlenecks. Here, we report the demonstration of this protocol in systems with one-dimensional and all-to-all connectivities on IBM's quantum hardware on up to 22 qubits, a regime which is presently inaccessible if post-selection is required. We demonstrate a collapse of the data into a scale-invariant form with critical exponents agreeing with theory within uncertainty. Our demonstration paves the way for studies of measurement-induced entanglement phase transitions and associated critical phenomena on larger near-term quantum systems.
Inferences for Random Graphs Evolved by Clustering Attachment

The evolution of random undirected graphs by the clustering attachment (CA) both without node and edge deletion and with uniform node or edge deletion is investigated. Theoretical results are obtained for the CA without node and edge deletion when a newly appended node is connected to two existing nodes of the graph at each evolution step. Theoretical results concern to (1) the sequence of increments of the consecutive mean clustering coefficients tends to zero; (2) the sequences of node degrees and triangle counts of any fixed node which are proved to be submartingales. These results were obtained for any initial graph. The simulation study is provided for the CA with uniform node or edge deletion and without any deletion. It is shown that (1) the CA leads to light-tailed distributed node degrees and triangle counts; (2) the average clustering coefficient tends to a constant over time; (3) the mean node degree and the mean triangle count increase over time with the rate depending on the parameters of the CA. The exposition is accompanied by a real data study.
XProspeCT: CT Volume Generation from Paired X-Rays

Computed tomography (CT) is a beneficial imaging tool for diagnostic purposes. CT scans provide detailed information concerning the internal anatomic structures of a patient, but present higher radiation dose and costs compared to X-ray imaging. In this paper, we build on previous research to convert orthogonal X-ray images into simulated CT volumes by exploring larger datasets and various model structures. Significant model variations include UNet architectures, custom connections, activation functions, loss functions, optimizers, and a novel back projection approach.
Global solutions of the 3D incompressible inhomogeneous viscoelastic system

In this paper, we prove the global existence of strong solutions for the 3D incompressible inhomogeneous viscoelastic system. We do not assume the"initial state"assumption and the"div-curl"structure inspired by the works [59,61]. It is a key to transform the original system into a suitable dissipative system by introducing a new effective tensor, which is useful to establish a series of energy estimates with appropriate time weights.