Miracle-dz/UniFAR-FTUs huggingface dataset:
DuKA: A Dual-Keyless-Attention Model for Multi-Modality EHR Data Fusion and Organ Failure Prediction

Objective: Organ failure is a leading cause of mortality in hospitals, particularly in intensive care units. Predicting organ failure is crucial for clinical and social reasons. This study proposes a dual-keyless-attention (DuKA) model that enables interpretable predictions of organ failure using electronic health record (EHR) data. Methods: Three modalities of medical data from EHR, namely diagnosis, procedure, and medications, are selected to predict three types of vital organ failures: heart failure, respiratory failure, and kidney failure. DuKA utilizes pre-trained embeddings of medical codes and combines them using a modality-wise attention module and a medical concept-wise attention module to enhance interpretation. Three organ failure tasks are addressed using two datasets to verify the effectiveness of DuKA. Results: The proposed multi-modality DuKA model outperforms all reference and baseline models. The diagnosis history, particularly the presence of cachexia and previous organ failure, emerges as the most influential feature in organ failure prediction. Conclusions: DuKA offers competitive performance, straightforward model interpretations and flexibility in terms of input sources, as the input embeddings can be trained using different datasets and methods. Significance: DuKA is a lightweight model that innovatively uses dual attention in a hierarchical way to fuse diagnosis, procedure and medication information for organ failure predictions. It also enhances disease comprehension and supports personalized treatment.
Challenging Interactions Between Patients With Severe Health Anxiety and the Healthcare System: A Qualitative Investigation

Objective: Patients with severe health anxiety have complex interpersonal relationships with medical providers and others in their social context, often resulting in conflictual interactions with providers and perception of poor medical care. An adequate understanding of the causes and consequences of these interactions is lacking, particularly 1 informed by the experience of the patient. This study used qualitative methods to explore the development and maintenance of health anxiety from the perspective of patients with lived experience of coping with health anxiety and their interactions with the healthcare system. Method: We conducted qualitative interviews with 11 primary care patients purposely sampled to describe their experience living with health anxiety, provider interactions, and social and family interactions surrounding health and health anxiety. We extracted themes related to living with health anxiety and interactions with providers and other significant relationships. Results: Thematic content analysis revealed 5 themes including 3 causal themes, 1 response theme, and 1 theme reflecting factors that mitigate health anxiety. Causal themes included subthemes reflecting predisposing factors of the self, key stimulus events from patient learning history, and maladaptive social interaction factors. The response theme was comprised of 2 subthemes: logical conclusions and health anxiety symptoms. The mitigating factors theme included subthemes of a trusting care relationship and recognition of disconfirming evidence. Conclusion: The themes and constituent subthemes identified in this study largely map onto cognitive-behavioral theory of health anxiety, demonstrating alignment between patient experience and theory. The resulting model also identifies potential points of intervention in the developmental and maintenance process. We provide recommendations to maximize those points of intervention.
Theistareykir revisited

Postglacial basalts from Theistareykir (younger than 10,000 years), northern Iceland, define the depleted end of the spectrum of chemical and isotopic compositions observed in Icelandic volcanics but extend to some of the most enriched chemical and isotopic compositions found in Icelandic tholeiites. A spectacular feature of these basalts is the impressive correlations observed between radiogenic isotope ratios (Sr, Nd, Hf, and Pb) and almost the entire spectrum of major and trace element concentrations and ratios. The radiogenic isotope and major and trace element compositions are little affected by crystal fractionation and are essentially unaffected by interaction with the preexisting crust. The Theistareykir basalts must therefore be relatively close in composition to primary melts from the mantle. Consequently, their chemical and isotopic compositions provide a unique opportunity to investigate the nature of melting beneath Iceland and the geochemical character and origin of the mantle source. Large variations in incompatible element abundances require source heterogeneity, as well as variable extents of melting, to be important factors in determining the final chemical composition of the melts. Melting integrates over a large pressure range and is dominated by melting a depleted peridotite similar to the ambient depleted North Atlantic mantle. The isotopically enriched component is of relatively minor abundance and probably has a lower solidus temperature compared to the depleted component. More than one isotopically enriched component must be involved, but it is difficult to identify the end‐member compositions using those of the lavas because of preeruptive averaging and damping of the enriched isotopic signals by mixing with the ambient depleted mantle or melts thereof, suggesting that the isotopic signals in Icelandic melts represent a somewhat muted isotopic signal of the enriched component(s) in the Icelandic source mantle. Comparison of the isotopic arrays of Icelandic basalts with those of global OIB suggests that the dominant enriched component may have a HIMU (high μ) affinity rather than representing a component similar to the enriched end of the Iceland isotopic arrays, and small amounts of an enriched component similar to enriched mantle (EMI)‐ type OIB sources are probably also involved.
TGF‐β signaling promotes desmoid tumor formation via CSRP2 upregulation

Abstract Desmoid tumors (DTs), also called desmoid‐type fibromatoses, are locally aggressive tumors of mesenchymal origin. In the present study, we developed a novel mouse model of DTs by inducing a local mutation in the Ctnnb1 gene, encoding β‐catenin in PDGFRA‐positive stromal cells, by subcutaneous injection of 4‐hydroxy‐tamoxifen. Tumors in this model resembled histologically clinical samples from DT patients and showed strong phosphorylation of nuclear SMAD2. Knockout of SMAD4 in the model significantly suppressed tumor growth. Proteomic analysis revealed that SMAD4 knockout reduced the level of Cysteine‐and‐Glycine‐Rich Protein 2 (CSRP2) in DTs, and treatment of DT‐derived cells with a TGF‐β receptor inhibitor reduced CSRP2 RNA levels. Knockdown of CSRP2 in DT cells significantly suppressed their proliferation. These results indicate that the TGF‐β/CSRP2 axis is a potential therapeutic target for DTs downstream of TGF‐β signaling.
Enhanced Velocity Modeling for a Geothermal Project in the Southern Vienna Basin – A Stacking Velocity Approach

Velocity models can be build based solely on or from a combination of checkshots, VSPs, sonic logs or seismic stacking velocities. Depending on the information available, the method of building a velocity model can vary (using interval velocities, average velocities, layer cake model, V0-K method, models based on geostatistical methods .). The advantages and disadvantages of these methods have been described by numerous authors. In the course of a geothermal project in the southern Vienna Basin, the problem of a time to depth conversion arose. In the area of interest, only six wells with checkshot-information were available and, therefore, the usage of a simple V0-K method or layer cake method was not suitable. Hence, the application of available seismic stacking velocities for velocity modeling was tested. The stacking velocities were converted into interval and average velocities using the Dix equation. These velocity values were then sampled into a geo-grid and spatially distributed in the grid using geostatistical methods. The stacking velocities were compared where checkshots or sonic logs were available. The result of this velocity modeling procedure was a 3D velocity cube that can be used to depth convert the seismic profiles and the interpretation from the time domain.
Family violence during COVID-19 and its impact on mental health of children: A systematic review

Purpose: The COVID-19 pandemic posed unanticipated challenges that could impact how the family system operates across the world. Restrictions imposed to control the rapid spread of the virus substantially increased violence in families. The current study aims to review violence in the family and its impact on the mental health of children during the pandemic. Method: A systematic search was conducted using keywords in the electronic databases PubMed, PsycINFO, and Web of Science, and a manual search was conducted on Google Scholar for articles from January 2020 to January 2021. Of the 50 records identified, seven studies that met eligibility criteria were selected for final analysis. Results: Results revealed that family violence during the pandemic has escalated the mental health problems of children, including aggressive and self-harming behaviours. Lockdown restrictions, social detachment, financial instability, fear of infection, and unemployment led to increased parental stress. Parents with a higher level of stress were more likely to maltreat their children. Conclusions: Exposure to short and long-term family violence can adversely impact the mental health of children and can negatively affect a child’s present and future life. Recommendations for researchers, mental health practitioners, public health authorities, and other service providers are also outlined.
Application of empirical and dynamical closure methods to simple climate models

This dissertation applies empiricallyand physically-based methods for closure of uncertain parameters and processes to three model systems that lie on the simple end of climate model complexity. Each model isolates one of three sources of closure uncertainty: uncertain observational data, large dimension, and wide ranging length scales. They serve as efficient test systems toward extension of the methods to more realistic climate models. The empirical approach uses the Unscented Kalman Filter (UKF) to estimate the transient climate sensitivity (TCS) parameter in a globally-averaged energy balance model. Uncertainty in climate forcing and historical temperature make TCS difficult to determine. A range of probabilistic estimates of TCS computed for various assumptions about past forcing and natural variability corroborate ranges reported in the IPCC AR4 found by different means. Also computed are estimates of how quickly uncertainty in TCS may be expected to diminish in the future as additional observations become available. For higher system dimensions the UKF approach may become prohibitively expensive. A modified UKF algorithm is developed in which the error covariance is represented by a reduced-rank approximation, substantially reducing the number of model evaluations required to provide probability densities for unknown parameters. The method estimates the state and parameters of an abstract atmospheric model, known as Lorenz 96, with accuracy close to that of a full-order UKF for 30-60% rank reduction. The physical approach to closure uses the Multiscale Modeling Framework (MMF) to demonstrate closure of small-scale, nonlinear processes that would not be resolved directly in climate models. A one-dimensional, abstract test model with a broad spatial spectrum is developed. The test model couples the Kuramoto-Sivashinsky equation to a transport equation that includes cloud formation and precipitation-like processes. In the test model, three main sources of MMF error are evaluated independently. Loss of nonlinear multi-scale interactions and periodic boundary conditions in closure models were dominant sources of error. Using a reduced order modeling approach to maximize energy content allowed reduction of the closure model dimension up to 75% without loss in accuracy. MMF and a comparable alternative model peformed equally well compared to direct numerical simulation.
TsImpute: an accurate two-step imputation method for single-cell RNA-seq data

Abstract Motivation Single-cell RNA sequencing (scRNA-seq) technology has enabled discovering gene expression patterns at single cell resolution. However, due to technical limitations, there are usually excessive zeros, called “dropouts,” in scRNA-seq data, which may mislead the downstream analysis. Therefore, it is crucial to impute these dropouts to recover the biological information. Results We propose a two-step imputation method called tsImpute to impute scRNA-seq data. At the first step, tsImpute adopts zero-inflated negative binomial distribution to discriminate dropouts from true zeros and performs initial imputation by calculating the expected expression level. At the second step, it conducts clustering with this modified expression matrix, based on which the final distance weighted imputation is performed. Numerical results based on both simulated and real data show that tsImpute achieves favorable performance in terms of gene expression recovery, cell clustering, and differential expression analysis. Availability and implementation The R package of tsImpute is available at https://github.com/ZhengWeihuaYNU/tsImpute.
THE SEISMICITY AND EARTHQUAKE FOCAL MECHANISMS OF THE BAIKAL RIFT ZONE 515MICITE ET MECANI5ME5 AU FOYER DE LA ZONE DE RIFT DU BAiKAL

Epicentres of earthquakes occurring in the region of the Baikal Rift Zone have a fractal distribution. Temporal variations of the fractal distri­ bution of the epicentral fields of the South Baikal and Tunka depres­ sions show that the spatial structure of the fields is still developing. For practically all regions of the Baikal Rift Zone, the seismic fields typical­ ly have clearly defined similarities at different levels of spatial hierarchy and across a wide energy range of earthquakes The index of seismi­ city at various scales varies over the zone, with the rift extremities being characterized by the greatest contrast. In this case, even within rela­ tively small areas, there are always places in which the level of seismic activity is less than in the neighbouring areas by a factor of 3 to 12. Analysis of the orientation of the kinematic P and T axes, esta­ blished from the focal mechanisms of more than 3000 earthquakes which occurred in the Baikal Rift Zone between 1950 and 1991, reveals a clear axial symmetry of the kinematic field. The axis of symmetry, which runs through the northern part of Lake Baikal, divides the area into two parts, mirror images of each other. The transition between the extensive regional kinematic field of rift style and the global compres­ sive kinematic field typical of Western Mongolia and Southern Yakutia is characterized by the existence of aseismic zones, symmetrically locat­ ed at both extremities of the Baikal Rift Zone.
Gut microbiota signatures in inflammatory bowel disease

Abstract Background Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence. Objectives Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re‐analyze publicly available fecal microbiota data from IBD patients. Methods We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta‐analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms. Results Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found. Conclusions Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.
Why does Listeria monocytogenes survive in food and food-production environments?

Abstract Listeria monocytogenes is one of the most dangerous food-borne pathogens and is responsible for human listeriosis, a severe disease with a high mortality rate, especially among the elderly, pregnant women and newborns. Therefore, this bacterium has an important impact on food safety and public health. It is able to survive and even grow in a temperature range from -0.4°C to 45°C, a broad pH range from 4.6 to 9.5 and at a relatively low water activity (aW < 0.90), and tolerates salt content up to 20%. It is also resistant to ultraviolet light, biocides and heavy metals and forms biofilm structures on a variety of surfaces in food-production environments. These features make it difficult to remove and allow it to persist for a long time, increasing the risk of contamination of food-production facilities and ultimately of food. In the present review, the key mechanisms of the pathogen’s survival and stress adaptation have been presented. This information may grant better understanding of bacterial adaptation to food environmental conditions.
Antibodies against advanced glycation end product Nepsilon-(carboxymethyl)lysine in healthy controls and diabetic patients.

AIMS/HYPOTHESIS Nepsilon-(carboxymethyl)lysine (CML) is one of the end products of protein glycoxidation and its accumulation is associated with diabetes complications. Since CML-modified proteins are immunogenic, we have investigated the presence of anti-CML antibodies in diabetic patients. METHODS Antibodies against CML-modified human serum albumin (HSA) were measured by direct enzyme-linked immunosorbent assay in the sera from 289 non-selected diabetic and in 120 healthy control subjects. RESULTS Immunoglobulin-G reactivity towards CML-HSA was significantly higher in diabetic than in control sera. The presence of anti-CML IgG in diabetics, however, was not influenced by age, duration of disease or glycaemic control. Analysis of distribution frequency revealed that anti-CML IgG in both control and diabetic subjects were not normally distributed and that the distribution curves were similar in the two groups. Moreover, only 14% of the diabetic subjects displayed antibody binding to CML-HSA above 95 centile in the control cohort. Competition experiments confirmed that the IgG detected in both control and diabetic groups were specific for CML epitopes and did not recognise glycated-HSA in which CML formation was inhibited. CONCLUSION/INTERPRETATION The presence of anti-CML IgG in diabetic sera is probably not related to the development of an immune response against protein glycoxidation products.
Rare presentation of pneumothorax in a young woman with underlying congenital pulmonary airway malformation

Congenital pulmonary airway malformation (CPAM) is the most common among a rare group of congenital anomalies of the lower respiratory tract. It has variable presentation depending on its subtype and the patient’s age. It may lead to respiratory distress in neonates. It can be a particularly challenging diagnosis in children born asymptomatic but present with complications later in life such as haemoptysis, recurrent chest infections, breathlessness and pneumothorax. Prenatal ultrasound, chest X-ray, CT scan and MRI are helpful in making a radiological diagnosis. A woman in her late teens presented with shortness of breath and right pleuritic chest pain. CT’s chest showed a number of bullae of varying sizes on the right, including one huge bulla compressing all three lobes. She underwent lung volume reduction surgery via video-assisted thoracoscopy, and the histology specimen confirmed the diagnosis of CPAM type 1.
HPV testing as an effective triage strategy in the follow-up after fertility-sparing treatment for glandular lesions of the uterine cervix

Objective The management and surveillance of glandular pre-cancerous lesions of the uterine cervix present distinct challenges compared with squamous lesions, primarily attributed to the lower effectiveness of diagnostic methods such as cytology or colposcopy. This study aimed to investigate the long-term safety of fertility-sparing treatment for adenocarcinoma in situ and microinvasive adenocarcinoma of the cervix, while identifying factors associated with recurrence, with a particular emphasis on the role of human papillomavirus (HPV) testing. Methods We retrospectively reviewed data from all patients with histopathologically confirmed adenocarcinoma in situ or microinvasive cervical adenocarcinoma who received treatment at a single center between 2002 and 2023. The study involved the examination of consecutive surgical specimens and the follow-up details. Factors associated with recurrence were assessed in a subgroup of patients with available long-term follow-up data (at least 6 months). Results In total, 143 patients (112 with adenocarcinoma in situ and 31 with adenocarcinoma) were included in the analysis. Among the 86 patients who underwent fertility-sparing treatment, the recurrence rate was 9% (12% for adenocarcinoma in situ and 4% for adenocarcinoma) during a median follow-up period of 56.6 months (range 7–179). No patients who were HPV negative experienced recurrence during the follow-up period. In contrast, among patients who were HPV positive, the recurrence rate was 38%. Additionally, HPV 16/18 positivity displayed a notable association with a higher risk of recurrence compared with the other high-risk genotypes, although this difference did not reach statistical significance (83% vs 10%; p=0.083, log-rank). Conclusion Our retrospective study demonstrated a significant association between the risk of recurrence and HPV status during the follow-up period. Consequently, long-term follow-up utilizing HPV testing and genotyping appears to be a secure alternative to a hysterectomy.