Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel variable neighborhood search approach for cell clustering for spatial transcriptomics

This paper introduces a new approach to cell clustering using the Variable Neighborhood Search (VNS) metaheuristic. The purpose of this method is to cluster cells based on both gene expression and spatial coordinates. Initially, we confronted this clustering challenge as an Integer Linear Programming minimization problem. Our approach introduced a novel model based on the VNS technique, demonstrating the efficacy in navigating the complexities of cell clustering. Notably, our method extends beyond conventional cell-type clustering to spatial domain clustering. This adaptability enables our algorithm to orchestrate clusters based on information gleaned from gene expression matrices and spatial coordinates. Our validation showed the superior performance of our method when compared to existing techniques. Our approach advances current clustering methodologies and can potentially be applied to several fields, from biomedical research to spatial data analysis.
The impact of isolated obesity compared with obesity and other risk factors on risk of stillbirth: a retrospective cohort study

Background: Maternal obesity is associated with stillbirth, but uncertainty persists around the effects of higher obesity classes. We sought to compare the risk of stillbirth associated with maternal obesity alone versus maternal obesity and additional or undiagnosed factors contributing to high-risk pregnancy. Methods: We conducted a retrospective cohort study using the Better Outcomes Registry and Network (BORN) for singleton hospital births in Ontario between 2012 and 2018. We used multivariable Cox proportional hazard regression and logistic regression to evaluate the relationship between prepregnancy maternal body mass index (BMI) class and stillbirth (reference was normal BMI). We treated maternal characteristics and obstetrical complications as independent covariates. We performed mediator analyses to measure the direct and indirect effects of BMI on stillbirth through major common-pathway complications. We used fully adjusted and partially adjusted models, representing the impact of maternal obesity alone and maternal obesity with other risk factors on stillbirth, respectively. Results: We analyzed data on 681 178 births between 2012 and 2018, of which 1956 were stillbirths. Class I obesity was associated with an increased incidence of stillbirth (adjusted hazard ratio [HR] 1.55, 95% confidence interval [CI] 1.35–1.78). This association was stronger for class III obesity (adjusted HR 1.80, 95% CI 1.44–2.24), and strongest for class II obesity (adjusted HR 2.17, 95% CI 1.83–2.57). Plotting point estimates for odds ratios, stratified by gestational age, showed a marked increase in the relative odds for stillbirth beyond 37 weeks’ gestation for those with obesity with and without other risk factors, compared with those with normal BMI. The impact of potential mediators was minimal. Interpretation: Maternal obesity alone and obesity with other risk factors are associated with an increased risk of stillbirth. This risk increases with gestational age, especially at term.
Overt and occult hepatitis B virus infection detected among chronic kidney disease patients on haemodialysis at a Tertiary Hospital in Ghana

Hepatitis B virus (HBV) infection is endemic in Ghana and chronic kidney disease patients on haemodialysis are a high-risk group for HBV infection. We determined the prevalence of overt and occult HBV infection among haemodialysis patients at the Korle Bu Teaching Hospital in Ghana. 104 consenting End Stage Renal Disease patients on long-term haemodialysis were recruited for the study and their socio-demographic, clinical and laboratory information were obtained using structured questionnaire. All the participants were tested for the hepatitis B surface antigen (HBsAg). The HBsAg-negative participants were re-tested for hepatitis B surface antibody (HBsAb), hepatitis B core antibody (HBcAb) and HBV DNA using chemiluminescence and Roche COBAS Ampli-Prep/TaqMan analyser and real-time polymerase chain reaction. Eight (7.7%) of the total participants were positive for HBsAg. Among the 96 HBsAg-negative participants, 12.5% (12) were HBcAb-positive, 7.3% (7) had detectable HBV DNA (mean = 98.7±53.5 IU/mL) and 40.6% (39) were positive for HBsAb. Five out of the 7 HBV DNA-positive participants were males and only one participant was negative for HBcAb. Seventy-three out of the 96 HBsAg-negative participants were vaccinated and 37 of these vaccinated individuals had significant HBsAb titres (mean = 423.21± 380.72 IU/mL). Our data demonstrated that the prevalence of overt and occult HBV infection among the haemodialysis (HD) patients was 7.7% and 7.3%, respectively, and only 50.7% of those who showed proof of vaccination were protected from HBV infection.
Amplified winter Arctic tropospheric warming and its link to atmospheric circulation changes

Abstract The physical cause of amplified deep Arctic tropospheric warming in winter in the Barents–Kara Seas (BKS) is examined. The authors propose that changes in the atmospheric circulation patterns are important for deep Arctic tropospheric warming in winter. It is found that the retrograde Urals blocking (UB) event concurrent with a negative North Atlantic Oscillation (NAO−) that arises from a prior negative Arctic Oscillation (AO−) is not favorable for tropospheric warming because of less water vapor over the BKS. Such UB events are related to more winter BKS sea ice associated with the negative sea surface temperature (SST) anomaly in the BKS. In contrast, a UB occurring together with a positive North Atlantic Oscillation (NAO+) shows less movement and can significantly enhance tropospheric warming over the BKS through increasing tropospheric sensible heat energy due to a persistent BKS water vapor increase. This type of quasi-stationary UB event is related to prior less BKS sea ice associated with a positive BKS SST anomaly that coexists with the North Atlantic SST tripole structure. In summary, because warm, wet and low sea-ice winters in the BKS are related to UB events with an NAO+, and depend on the winter prior sea-ice condition, the tropospheric warming is to some extent a manifestation of the sea-ice–blocking–moisture feedback in the BKS.
COMP 562 Project Report : An Evaluation of the Pyramid Stereo Matching Network ( PSMNet )

Recent work proposed by Jia-Ren Chang and Yong-Shen Chen has suggested that Pyramid Stereo Matching (PSM) Network, can potentially be an efficient solution to robust and accurate 3D reconstructions. The purpose of our project is to evaluate the performance of the PSMNet on different combinations of datasets and then to seek potential improvements for the network. To achieve the goals, we will test the PSMNet first by validating pre-trained network on public dataset such as KITTI 2012 and KITTI 2015 and then training and testing on two synthetic datasets generated by ourselves. During the evaluation, we would like to see the robustness and accuracy of PSMNet in various scenes. We also propose to add additional training layers to enhance network performance.
Bifidobacterium alleviate metabolic disorders via converting methionine to 5’-methylthioadenosine

ABSTRACT Dietary patterns and corresponding gut microbiota profiles are associated with various health conditions. A diet rich in polyphenols, primarily plant-based, has been shown to promote the growth of probiotic bacteria in the gastrointestinal tract, subsequently reducing the risk of metabolic disorders in the host. The beneficial effects of these bacteria are largely due to the specific metabolites they produce, such as short-chain fatty acids and membrane proteins. In this study, we employed a metabolomics-guided bioactive metabolite identification platform that included bioactivity testing using in vitro and in vivo assays to discover a bioactive metabolite produced from probiotic bacteria. Through this approach, we identified 5’-methylthioadenosine (MTA) as a probiotic bacterial-derived metabolite with anti-obesity properties. Furthermore, our findings indicate that MTA administration has several regulatory impacts on liver functions, including modulating fatty acid synthesis and glucose metabolism. The present study elucidates the intricate interplay between dietary habits, gut microbiota, and their resultant metabolites.
Evaluation of the diagnostic utility of MCAM-1 (CD146) in a group of common gynecological cancers: A case-control study

Objective: MCAM-1 (CD146) is an endothelial cell adhesion molecule belonging to the immunoglobulin superfamily. Recent studies have identified CD146 expression as a critical marker for tumor progression, migration, and metastasis in various malignancies. This study aimed to evaluate CD146 immunohistochemical expression in various gynecological cancers. Materials and Methods: This study was conducted in a tertiary medical center in central India. A total of 49 gynecological cancer cases and 16 site-matched controls were included. The cases comprised 27 cervical, 10 endometrial, 10 ovarian, and two miscellaneous cancers. CD146 immunohistochemistry was performed and assessed for immunoreactivity score (IRS), microvascular density (MVD), and microvascular caliber (MVC). An IRS of 5 or more was considered CD146 positive. Results: The p-values for CD146 positivity for cases vs. control were 0.0531, 0.0580, and 0.007 for cervical, endometrial, and ovarian sites, respectively. The mean MVD was found to be significantly higher in cases compared with benign tissues (p-value <0.00001), and the mean MVC of cases was found to be smaller when compared with the controls (p-value <0.0001). Conclusion: MVD by CD146 was found to be higher in gynecological malignancies, highlighting its role in cancer neo-angiogenesis and its potential therapeutic role. CD146 epithelial expression was also significantly higher in ovarian cancers. Further studies with a larger sample size are required to confirm that this protein may be a potential theognostic target in gynecological cancers.
Integrating chemistry, fluid flow, and mechanics to drive spontaneous formation of three-dimensional (3D) patterns in anchored microstructures

Significance Through modeling, we show that enzymatic reactions on flexible microposts in solution inherently generate reaction-convection processes, which provide untapped approaches for regulating the spatiotemporal behavior of soft matter in fluids. Through self-generated fluid flows, the posts form distinct “fingerprints” that characterize the properties of that given system. Each variation in the system’s features leads to the formation of a different fingerprint. Hence, the system constitutes a sensor, allowing specific chemicals to be identified through the formation of specific patterns. The posts also display kaleidoscopic behavior, where one structure controllably morphs into another, enabling one material to perform multiple tasks. The findings reveal how reaction-convection processes involving immersed posts produce a distinctive interplay among chemistry, hydrodynamics and fluid-structure interactions.
Search for Microphysical Signatures of Stochastic Condensation in Marine Boundary Layer Clouds Using Airborne Digital Holography

Droplet growth due to stochastic condensation has been considered as one of the mechanisms to cause broadening of cloud droplet size distributions and jump the bottleneck between droplet growth due to diffusion and collision‐coalescence. Digital in‐line holography is used to measure variations in droplet number concentration and droplet size in marine boundary layer clouds. Distributions of phase relaxation times are quite broad for some clouds. Turbulence correlation times are estimated, and the comparison of these with phase relaxation times suggests that clouds exist in both fast and slow microphysical regimes. Presumed signatures of stochastic condensation, such as increasing relative size dispersion and increasing droplet size with decreasing number density, are observed.
Analytical model for environmental tracer transport in well catchments

In this paper, we present analytical solutions and discuss them for simplified groundwater systems with decaying environmental tracers such as 3H, including the formation of a decay product such as tritiogenic 3He. The developed solutions are applicable for shallow, unconfined groundwater systems, which can be conceptually described by a steady‐state, two‐dimensional, semiconfined groundwater flow model with constant thickness, recharge rate, and porosity. The prerequisite for the applicability of our solutions is that the pumping wells and observation wells at which tracer information is available are fully screened over the entire aquifer thickness. The sampling by pumping from such wells produces the complete mixing of water of different age and origin. The application of our solution to the Baltenswil (Zurich, Switzerland) groundwater field site shows that the simplified model is able to catch essential dynamics of the transient concentration development of 3H and 3He.
Influence of dominant wind patterns in a distal region of the NW Iberian Margin during the last glaciation

This work combines planktonic foraminiferal assemblages, stable isotope, transfer function estimated sea surface paleotemperatures (SST) and export productivity (Pexp) with sedimentological records from the PC7 core to document paleoclimatic and paleoceanographic changes on a distal region of the NW Iberian Margin since the last glaciation (<≈68 ka). Neodymium and strontium isotope data are also used to identify the provenance of ice rafted debris (IRD) during Heinrich event 5 (H5). Our results are compared and combined with previously published records and evidence that melt water and icebergs from the Canada, Greenland, Iceland and Europe ice sheets arrived to the NW Iberian Margin causing a significant decrease of SST during the last six Heinrich Stadials (HS) and some Dansgaard–Oeschger (D-O) stadial events. εNd and 87Sr/86Sr indicate that the studied locality mostly received sediments from European Ice Sheets (EIS) during H5. During the HS and D–O stadial events, SSTs were in general higher than in other cores collected in inner areas of the NW Iberian Margin. The presence and intensification of Portugal Current probably induced heat transfer to this distal region of the Iberian Margin. Our results also suggest the occurrence of high variability in the intensity and wind patterns during the last glaciation. In some periods, the intensity of northerly winds could have been very strong and contributed to a significant stimulation of ocean productivity in this distal area through the intensification of upwelling. In general, oceanic productivity decreased during the HS and D–O as the presence of cold and less saline water prevented nutrient rich waters from deep levels reaching the surface. The high productivity events were bracketed by periods characterized by the highest influence of the Azores Current eastern branch during which northerly winds and the oceanic productivity should have been weakened. Supplementary material: Geochemical and foraminiferal data analysed in this work as well as Pearson Correlations between the analysed data are available at https://doi.org/10.6084/m9.figshare. c.3931813
Rehabilitation in PRactice Promoting physical activity for individuals with neurological disability : indications for practice

Purpose: This study explored processes that influenced involvement in recreational exercise for individuals with neurological disability, to identify strategies to promote physical activity for health and well-being in this population. Method: Nineteen participants (11 males and eight females), aged 20–71 years, with a range of neurological conditions and functional limitations, were recruited in one large metropolitan area in New Zealand. Individual semi-structured interviews explored participants’ views, perceptions, and experiences of undertaking recreational exercise. Data were analysed for themes. Results: For some individuals, recreational exercise is undertaken for its physical, psychological, or social benefits, despite the physical activity itself feeling relatively unsatisfactory. In contrast, individuals who are able to undertake their preferred choice of recreational exercise experience intense satisfaction. This motivates selfmaintenance of physical activity, even for those individuals who require carer support or assistance to do so. Conclusions: This study has identified that there can be two forms of involvement in recreational exercise that allows individuals with neurological disability to become more physically active. The information could be further developed and tested in intervention studies to provide strategies for health professionals to facilitate engagement in physical activity for people with neurological disability.
Discovery of Red-Shifting Mutations in Firefly Luciferase Using High-Throughput Biochemistry

Photinus pyralis luciferase (FLuc) has proven a valuable tool for bioluminescence imaging, but much of the light emitted from the native enzyme is absorbed by endogenous biomolecules. Thus, luciferases displaying red-shifted emission enable higher resolution during deep-tissue imaging. A robust model of how protein structure determines emission color would greatly aid the engineering of red-shifted mutants, but no consensus has been reached to date. In this work, we applied deep mutational scanning to systematically assess 20 functionally important amino acid positions on FLuc for red-shifting mutations, predicting that an unbiased approach would enable novel contributions to this debate. We report dozens of red-shifting mutations as a result, a large majority of which have not been previously identified. Further characterization revealed that mutations N229T and T352M, in particular, bring about unimodal emission with the majority of photons being >600 nm. The red-shifting mutations identified by this high-throughput approach provide strong biochemical evidence for the multiple-emitter mechanism of color determination and point to the importance of a water network in the enzyme binding pocket for altering the emitter ratio. This work provides a broadly applicable mutational data set tying FLuc structure to emission color that contributes to our mechanistic understanding of emission color determination and should facilitate further engineering of improved probes for deep-tissue imaging.
Rubisco small subunit (RbCS) is co-opted by potyvirids as the scaffold protein in assembling a complex for viral intercellular movement

Plant viruses must move through plasmodesmata (PD) to complete their life cycles. For viruses in the Potyviridae family (potyvirids), three viral factors (P3N-PIPO, CI, and CP) and few host proteins are known to participate in this event. Nevertheless, not all the proteins engaging in the cell-to-cell movement of potyvirids have been discovered. Here, we found that HCPro2 encoded by areca palm necrotic ring spot virus (ANRSV) assists viral intercellular movement, which could be functionally complemented by its counterpart HCPro from a potyvirus. Affinity purification and mass spectrometry identified several viral factors (including CI and CP) and host proteins that are physically associated with HCPro2. We demonstrated that HCPro2 interacts with both CI and CP in planta in forming PD-localized complexes during viral infection. Further, we screened HCPro2-associating host proteins, and identified a common host protein in Nicotiana benthamiana–Rubisco small subunit (NbRbCS) that mediates the interactions of HCPro2 with CI or CP, and CI with CP. Knockdown of NbRbCS impairs these interactions, and significantly attenuates the intercellular and systemic movement of ANRSV and three other potyvirids (turnip mosaic virus, pepper veinal mottle virus, and telosma mosaic virus). This study indicates that a nucleus-encoded chloroplast-targeted protein is hijacked by potyvirids as the scaffold protein to assemble a complex to facilitate viral movement across cells.
Comparative evaluation of lateral flow assays to diagnose chronic Trypanosoma cruzi infection in Bolivia

Bolivia has the highest incidence of Chagas disease (CD) worldwide. Caused by the parasite Trypanasoma cruzi, CD is generally a chronic condition. Diagnosis is logistically and financially challenging, requiring at least two different laboratory-based serological tests. Many CD cases are missed; in Bolivia it is estimated just 6% of individuals chronically infected with T. cruzi get diagnosed. Achieving control on the way to elimination of CD requires a radical simplification of the current CD testing pathways, to overcome the barriers to accessing CD treatment. We aimed to generate unbiased performance data of lateral flow assays (LFAs) for T. cruzi infection in Bolivia, to evaluate their usefulness for improving T. cruzi diagnosis rates in a precise and efficient manner. This retrospective, laboratory-based, diagnostic evaluation study sought to estimate the sensitivity/specificity of 10 commercially available LFAs for T. cruzi, using the current CD diagnostic algorithm employed in Bolivia as the reference test method. All tests were blinded at the study site and performed by three operators. In total, 470 serum samples were tested, including 221 and 249 characterized as CD-positive/-negative, respectively. The LFAs were scored according to their relative importance using a decision-tree-based algorithm, with the mean decrease in Gini index as the scoring metric. The estimates of sensitivities ranged from 62.2–97.7% (95% confidence interval (CI) lower bound 55.0–94.7%); for specificities the range was 78.6–100% (95% CI lower bound 72.0–97.5%); 5/10 and 6/10 tests had sensitivity >90% and specificity >95%, respectively. Four LFAs showed high values of both sensitivity (93–95%) and specificity (97–99%). The agreement between 6 LFAs and the reference tests was almost perfect (Kappa 0.83–0.94). Most LFAs evaluated thus showed performances comparable with current laboratory-based diagnostic methods.