Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms of development and progression of pancreatic neoplasms

Pancreatic ductal adenocarcinoma (PDAC) develops via dysplastic changes in the epithelia graded as low‐ and high‐grade with accumulation of molecular alterations. Constitutive activation of mitogen‐activated protein kinase (MAPK) contributed by attenuation of DUSP6 plays a key role in sustaining PDAC. Active MAPK induces various molecules that function as effectors to sustain PDAC. AURKA and SON are downstream effectors that contribute substantially to the proliferation and survival of PDAC cells and are potentially useful as therapeutic targets. Active MAPK also promote microRNAs that modulate the proliferation of PDAC cells and are useful as diagnostic markers. Familial pancreatic cancer kindreds in Japan show various germline mutations supposed to increase a pancreatic cancer risk. Intraductal papillary mucinous neoplasms (IPMNs) consist of dilated ducts lined by papillary neoplastic epithelia of various shapes and varying grades of atypia. Various papillae of IPMNs are classified into four subtypes that are associated with clinicopathological features, including patient prognosis. GNAS is a specific driver gene for the development of IPMN through gain‐of‐function mutations. Tracing of molecular alterations has elucidated the mechanism of progression of IPMN from dysplasia to carcinoma, as well as one type of papillae. Intraductal tubulopapillary neoplasms belong to a distinct class of pancreatic neoplasms.
Model Order Reduction Techniques for Uncertainty Quantification Problems

Keywords: uncertainty quantification ; stochastic partial different equations ; sparse approximation ; stochastic collocation method ; reduced basis method ; reliability analysis ; stochastic optimal control These Ecole polytechnique federale de Lausanne EPFL, n° 6118 (2014)Programme doctoral MathematiquesFaculte des sciences de baseInstitut de mathematiques des sciences computationnelles et ingenierieChaire de modelisation et calcul scientifiqueJury: Prof. T. Mountford (president) ; Prof. A. Quarteroni, Dr G. Rozza (directeurs) ; Prof. J.S. Hesthaven, Prof. Y. Maday, Prof. T. Yizhao Hou (rapporteurs) Public defense: 2014-5-15 Reference doi:10.5075/epfl-thesis-6118Print copy in library catalog Record created on 2014-05-05, modified on 2017-05-12
CO(1-0) emission from luminous infrared galaxies in the southern hemisphere

Les observations radio de 33 galaxies sud, de flux IR > 4.5 Jy et de luminosite IR intrinseque > 1O 11 L ○. , sont presentees. Une emission CO (1-0) est detectee dans 28 de ces galaxies. Les profils de CO sont analyses. Le centroide des vitesses heliocentriques du profil CO, l'intensite totale de la raie CO et la masse totale de l'hydrogene moleculaire sont determines pour chacune des 28 galaxies.
The effect of metabolic syndrome on controlled ovarian stimulation outcome in infertile women with polycystic ovary syndrome undergoing assisted reproductive technology cycles

ABSTRACT Objective: To evaluate the effect of metabolic syndrome (MetS) diagnosis on oocyte quality and pregnancy outcomes in infertile women with polycystic ovary syndrome (PCOS) who undergoing antagonist-controlled ovarian stimulation (COS) and in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) cycles. Subject and methods: This prospective cohort study was conducted from November 2019 to November 2020 across two university-affiliated infertility centers in Iran. The PCOS diagnosis was defined according to the Rotterdam criteria. The patients prior to IVF/ICSI cycles were evaluated for MetS diagnosis. MetS was detected according to the National Cholesterol Education Program/Adult Treatment Panel III with the presence of at least three or more of the specific clinical criteria. The cycle outcomes were compared between MetS and non-MetS groups. Results: Overall, 68 eligible infertile PCOS patients with MetS diagnosis and 126 without MetS participated. The MetS diagnosis was associated with the increased requirement of gonadotropins and the COS duration significantly (P = 0.001). Although the total numbers of retrieved and MII oocytes, obtained and top-quality embryos as well as clinical pregnancy and live birth rates in the MetS group were lower than those of in the non-MetS group, the differences were not statistically significant (P > 0.05). In follow-up of the obstetrics complications, the rate of preeclampsia was significantly higher in patients with MetS (P = 0.02). Conclusion: MetS diagnosis in PCOS patients was associated with non-significant poor COS and pregnancy outcome. Further studies with larger sample sizes are recommended to clarify the risk of MetS in patients undergoing ART cycles.
Real-world evidence of quality of life improvement in patients with distal ulcerative colitis treated by mesalazine: the Quartz study

Background Distal ulcerative colitis (UC) is responsible for distressing symptoms and reduces quality of life (QoL). Oral and topical formulations of 5-amino-salicylic acid are the first line therapy for mild to moderate distal UC. Objective Our aim was to evaluate the impact of mesalazine treatment for mild to moderate ulcerative proctitis and proctosigmoiditis on patient QoL. Methods Ninety-three patients with mild to moderate ulcerative proctitis and proctosigmoiditis, initiating a treatment with Pentasa, were prospectively included. The primary endpoint was the change from baseline to W8 in patient health-related QoL (HRQoL) as measured by the Short Inflammatory Bowel Disease Questionnaire (SIBDQ) total score. Results More than 80% of patients were prescribed with a rectal formulation, either alone (47.9%) or with an oral formulation (35.1%), and 17.0% of patients were prescribed oral formulation alone. Mean SIBDQ score was improved at W8 in patients affected with mild and moderate disease (P < 0.001 versus baseline in both groups, as well as in patients who achieved clinical remission (P < 0.001). Patients who achieved clinical remission at W8 reached a mean change of +6.7 (±7.1), whereas those who did not achieve clinical remission had a mean change of +1.1 (±8.9). Seventy-five per cent of patients had an improvement of their disability index at W8. Fecal incontinence was also improved at W8. Conclusion HRQoL measuring with the SIBDQ is proportionally related to disease activity in patients with distal UC treated with mesalazine.
Genomic novelty within a “great speciator” revealed by a high-quality reference genome of the collared kingfisher (Todiramphus chloris collaris)

Abstract Islands are natural laboratories for studying patterns and processes of evolution. Research on island endemic birds has revealed elevated speciation rates and rapid phenotypic evolution in several groups (e.g. white-eyes, Darwin’s finches). However, understanding the evolutionary processes behind these patterns requires an understanding of how genotypes map to novel phenotypes. To date, there are few high-quality reference genomes for species found on islands. Here, we sequence the genome of one of Ernst Mayr’s “great speciators,” the collared kingfisher (Todiramphus chloris collaris). Utilizing high molecular weight DNA and linked-read sequencing technology, we assembled a draft high-quality genome with highly contiguous scaffolds (scaffold N50 = 19 Mb). Based on universal single-copy orthologs, we estimated a gene space completeness of 96.6% for the draft genome assembly. The population demographic history analyses reveal a distinct pattern of contraction and expansion in population size throughout the Pleistocene. Comparative genomic analysis of gene family evolution revealed that species-specific and rapidly expanding gene families in the collared kingfisher (relative to other Coraciiformes) are mainly involved in the ErbB signaling pathway and focal adhesion. Todiramphus kingfishers are a species-rich group that has become a focus of speciation research. This draft genome will be a platform for future taxonomic, phylogeographic, and speciation research in the group. For example, target genes will enable testing of changes in sensory structures associated with changes in vision and taste genes across kingfishers.
Dual Polarization Modality Fusion Network for Assisting Pathological Diagnosis

Polarization imaging is sensitive to sub-wavelength microstructures of various cancer tissues, providing abundant optical characteristics and microstructure information of complex pathological specimens. However, how to reasonably utilize polarization information to strengthen pathological diagnosis ability remains a challenging issue. In order to take full advantage of pathological image information and polarization features of samples, we propose a dual polarization modality fusion network (DPMFNet), which consists of a multi-stream CNN structure and a switched attention fusion module for complementarily aggregating the features from different modality images. Our proposed switched attention mechanism could obtain the joint feature embeddings by switching the attention map of different modality images to improve their semantic relatedness. By including a dual-polarization contrastive training scheme, our method can synthesize and align the interaction and representation of two polarization features. Experimental evaluations on three cancer datasets show the superiority of our method in assisting pathological diagnosis, especially in small datasets and low imaging resolution cases. Grad-CAM visualizes the important regions of the pathological images and the polarization images, indicating that the two modalities play different roles and allow us to give insightful corresponding explanations and analysis on cancer diagnosis conducted by the DPMFNet. This technique has potential to facilitate the performance of pathological aided diagnosis and broaden the current digital pathology boundary based on pathological image features.
Stellar magnetic activity and Star-Planet Interactions (invited review)

Stellar magnetic activity is an important factor in the formation and evolution of exoplanets. Magnetic phenomena like stellar flares, coronal mass ejections, and high-energy emission affect the exoplanetary atmosphere and its mass loss over time. One major question is whether the magnetic evolution of exoplanet host stars is the same as for stars without planets; tidal and magnetic interactions of a star and its close-in planets may play a role in this. Stellar magnetic activity also shapes our ability to detect exoplanets with different methods in the first place, and therefore we need to understand it properly to derive an accurate estimate of the existing exoplanet population. Here I review recent theoretical and observational results, as well as outline some avenues for future progress.
Aluminum chloride induces G0/G1 phase arrest via regulating the reactive oxygen species-depended non-canonical STAT1 pathway in hFOB1.19 cells

Treatment with aluminum chloride (AlCl3) suppresses the growth of osteoblastic cells; however, the molecular mechanisms underlying the impact of AlCl3 on cell growth have not been fully characterized. In this study, we observed that exposure of hFOB1.19 cells to AlCl3 arrested cells at G0/G1 phase by inducing p21 expression. Further studies indicated that AlCl3 upregulated the phosphorylation level of signal transducer and activator of transcription 1 (STAT1) at serine 727 site (Ser727). By chromatin immunoprecipitation and electrophoretic mobility shift assay, we found that AlCl3 promoted STAT1/DNA binding activity to p21 promoter, thus resulting in the upregulation of p21. Moreover, siRNA-mediated knockdown of STAT1 attenuated p21 level induced by AlCl3. Notably, using hFOB1.19 cells stably expressing dominant-negative STAT1 (Ser727Ala), we demonstrated that phosphorylation of STAT1 at Ser727 site is required for p21-mediated cycle arrest induced by AlCl3. Mechanism investigation indicated that AlCl3 stimulated the phosphorylation of JNK, and administration of JNK inhibitor SP600125 prevented AlCl3-induced G0/G1 arrest through suppressing the phosphorylation of STAT1. Notably, pretreatment with N-acetyl-cysteine, a reactive oxygen species scavenger, conferred a significantly inhibitory effect on AlCl3-mediated activation of JNK/STAT1 signaling pathway. Taken together, our findings provide the molecular mechanism for G0/G1 arrest induced by AlCl3 in osteoblastic cells.
Real‐world data on lenalidomide dosing and outcomes in patients newly diagnosed with multiple myeloma: Results from the Canadian Myeloma Research Group Database

Using the Canadian Myeloma Research Group Database, a retrospective study of 167 newly diagnosed, transplant‐ineligible patients with multiple myeloma (MM) that received lenalidomide‐dexamethasone as front‐line treatment was conducted to understand the impact of lenalidomide dosing. Starting dose modifications were common, 42% of patients started on lenalidomide <25 mg with normal renal function. During treatment course, 35% of patients required further dose reduction. Dose reductions in the first year did not have an impact on progression free survival or overall survival. Further studies need to be conducted to understand the impact of dosing strategies of anti‐MM agents in the real world.
Recognition of Temporal Sequences of Patterns

Using an asymmetric associative network with synchronous updating, it is possible to recall a sequence of patterns. To obtain a stable sequence generation with a large storage capacity, we introduce a threshold that eliminates the contribution of weakly correlated patterns. For this system we find a set of evolution equations for the overlaps of the states with the patterns to be recognized. We solve these equations in the limit of the stationary cycle, and obtain the critical value of the capacity as a function of the threshold and temperature. Finally, a numerical simulation is made, confirming the theoretical results.
Neurophysiology tools to lower the stroke onset to treatment time during the golden hour: microwaves, bioelectrical impedance and near infrared spectroscopy

Abstract Reperfusion therapy administration timing in acute ischaemic stroke is the main determinant of patients’ mortality and long-term disability. Indeed, the first hour from the stroke onset is defined the “golden hour”, in which the treatment has the highest efficacy and lowest side effects. Delayed ambulance transport, inappropriate triage and difficulty in accessing CT scans lead to delayed onset to treatment time (OTT) in clinical practice. To date brain CT scan is needed to rule out intracranial haemorrhage, which is a major contraindication to thrombolytic therapy. The availability, dimension and portability make CT suitable mainly for intrahospital use, determining further delays in the therapies administration. This review aims at evaluating portable neurophysiology technologies developed with the scope of speeding up the diagnostic phase of acute stroke and, therefore, the initiation of intravenous thrombolysis. Medline databases were explored for studies concerning near infrared spectroscopy (NIRS), bioelectrical impedance spectroscopy (BIS) and Microwave imaging (MWI) as methods for stroke diagnosis. A total of 1368 articles were found, and 12 of these fit with our criteria and were included in the review. For each technology, the following parameters were evaluated: diagnostic accuracy, ability to differentiate ischaemic and haemorrhagic stroke, diagnosis time from stroke onset, portability and technology readiness level (TRL). All the described methods seem to be able to identify acute stroke even though the number of studies is very limited. Low cost and portability make them potentially usable during ambulance transport, possibly leading to a reduction of stroke OTT along with the related huge benefits in terms of patients outcome and health care costs. In addition, unlike standard imaging techniques, neurophysiological techniques could allow continuous monitoring of patients for timely intrahospital stroke diagnosis. KEY MESSAGES First hour from the stroke onset is defined the “golden hour”, in which the treatment has the highest efficacy and lowest side effects. The delay for stroke onset to brain imaging time is one of the major reasons why only a minority of patients with acute ischaemic stroke are eligible to reperfusion therapies. Neurophysiology techniques (NIRS, BIS and MWI) could have a potential high impact in reducing the time to treatment in stroke patients.
In vivo magnetic resonance 31P‐Spectral Analysis With Neural Networks: 31P‐SPAWNN

We have introduced an artificial intelligence framework, 31P‐SPAWNN, in order to fully analyze phosphorus‐31 ( 31$$ {}^{31} $$ P) magnetic resonance spectra. The flexibility and speed of the technique rival traditional least‐square fitting methods, with the performance of the two approaches, are compared in this work.
Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises

Significance Although strepsirrhines occupy a key node in primate phylogeny, our knowledge of this group remains quite limited. Here, we integrate comparative genomics analyses and functional assays to reveal the genetic underpinnings of evolutionary adaptation in the pygmy loris, a unique strepsirrhines group. We identified a series of genes that have contributed to certain distinctive adaptive traits of the pygmy loris, namely PITRM1 (low metabolic rate), MYOF (slow movement), and PER2 (hibernation). Our findings serve to deepen our understanding of the adaptive evolution of the strepsirrhines, and may also provide useful information for future studies of human disorders related to abnormal metabolism, skeletal muscle development, and circadian rhythms.
Employment Status and Work Functioning among Kidney Transplant Recipients

Visual Abstract Background and objectives To date, employment figures of kidney transplant recipients in Europe are inconsistent. Additionally, little is known about work functioning of employed kidney transplant recipients and work functioning trajectories before and after transplantation. Design, setting, participants, & measurements Data from the ongoing TransplantLines Biobank and Cohort study and from community-dwelling employed adults were used. Health-related work functioning of kidney transplant recipients was assessed with the Work Role Functioning Questionnaire 2.0 and compared with potential kidney donors and community-dwelling employed adults. Results We included 668 kidney transplant recipients of working age (59% men, age 51±11 years) at median 3 (interquartile range, 2–10) years after transplantation, 246 potential kidney donors of working age (43% men, age 53±9 years), and 553 community-dwelling employed adults (70% men, age 45±11 years). The proportion of employed kidney transplant recipients was lower compared with potential kidney donors (56% versus 79%). If employed, the work functioning score of kidney transplant recipients was slightly lower compared with employed potential kidney donors yet higher compared with community-dwelling employed adults (medians 91 [interquartile range, 76–98], 94 [interquartile range, 85–99], and 88 [interquartile range, 79–95], respectively). Backward linear regression analyses revealed that lower educational level, having a kidney from a deceased donor, presence of tingling or numbness of hands or feet, presence of concentration/memory problems, presence of anxiety, and presence of severe fatigue were independently associated with lower work functioning among kidney transplant recipients. Additional subgroup analyses showed that work functioning scores were lower before transplantation than at 12 months after transplantation (83 [interquartile range, 66–93] versus 92 [interquartile range, 88–98], respectively; P=0.002). Conclusions Stable employed kidney transplant recipients report to function well at work. In addition, this study shows that self-reported work functioning is higher after successful kidney transplantation compared with before transplantation. Clinical Trial registry name and registration number: TransplantLines Biobank and Cohort study, NCT03272841 Podcast This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2022_09_26_CJN05560522. mp3.
BIO-SYSTEMS AS SELF-ORGANIZING QUANTUM SYSTEMS

This book belongs to a series of online books summarizing the recent state Topological Geometrodynamics (TGD) and its applications. TGD can be regarded as a unified theory of fundamental interactions but is not the kind of unified theory as so called GUTs constructed by graduate students at seventies and eighties using detailed recipes for how to reduce everything to group theory.
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome

Abstract Chemical probes are important tools to investigate the function of proteins, evaluate their potential as therapeutic targets and provide chemical starting points for drug discovery. As a result, a growing federation of scientists aims to generate chemical probes for all human druggable proteins. A diverse array of data typically guides target selection and chemical probe discovery: information on protein function can help prioritize targets, domain architecture can provide insight on druggability, structural data enables molecular design and existing chemical ligands can serve as foundation or inspiration for chemical probe development. But these heterogenous data types are dispersed across a variety of public repositories that are difficult to cross-reference by non-experts. We developed ChemBioPort, an online resource that allows users to combine queries related to the ontology, domain architecture or name of human proteins to produce downloadable tables that integrate information on function, disease association, essentiality, tissue enrichment, domain architecture, structure and chemical ligands of proteins. Users can convert these tables into dendrograms reflecting sequence similarity, onto which they can graphically project all data types, linked via a mouse-click to their original repositories or published articles. This interface will support the growing community of chemical biologists, chemists, cell and structural biologists on their perilous journey from genes to medicines. Database URL: https://chembioport.thesgc. org
A Study Towards a Dynamic Theory of Seasonality for Economic Time Series

Traditionally One Decomposes Economic Time Series Exhibiting Seasonality in a Cyclical Component, a Seasonal Component and Possibly Other Components. the Fundamental Assumptions Almost Exclusively Made About This Decomposition Is That (1) the Components Are Mutually Orthogonal and (2) the Seasonal Component Has Power Only At the Seasonal Frequency and Its Harmonics. in This Paper We Discuss the Fact That in the Context of Dynamic Economic Models Such a Decomposition Is Usually Inappropriate for the Endogenous Variables of the Model. We Discuss Three Possible Decompositions, Including the Traditional Decomposition, Analyze Their Properties and Digress on the Relevant Use of the Decompositions We Define. the Paper Also Discusses Ways to Estimate Dynamic Models with Seasonality, Yielding the Relevant Decomposition, Via the Mle Approach. It Is Shown That the Traditional Decomposition of an Endogenous Variable Typically Does Not Coincide with What We Believe Is a Relevant Decomposition of That Variable Along the Lines of the Exogenous Seasonal and Cyclical Sources of the Model.