Miracle-dz/UniFAR-FTUs huggingface dataset:
Mucosal microbiome dysbiosis in gastric carcinogenesis

Objectives We aimed to characterise the microbial changes associated with histological stages of gastric tumourigenesis. Design We performed 16S rRNA gene analysis of gastric mucosal samples from 81 cases including superficial gastritis (SG), atrophic gastritis (AG), intestinal metaplasia (IM) and gastric cancer (GC) from Xi’an, China, to determine mucosal microbiome dysbiosis across stages of GC. We validated the results in mucosal samples of 126 cases from Inner Mongolia, China. Results We observed significant mucosa microbial dysbiosis in IM and GC subjects, with significant enrichment of 21 and depletion of 10 bacterial taxa in GC compared with SG (q<0.05). Microbial network analysis showed increasing correlation strengths among them with disease progression (p<0.001). Five GC-enriched bacterial taxa whose species identifications correspond to Peptostreptococcus stomatis, Streptococcus anginosus, Parvimonas micra, Slackia exigua and Dialister pneumosintes had significant centralities in the GC ecological network (p<0.05) and classified GC from SG with an area under the receiver-operating curve (AUC) of 0.82. Moreover, stronger interactions among gastric microbes were observed in Helicobacter pylori-negative samples compared with H. pylori-positive samples in SG and IM. The fold changes of selected bacteria, and strengths of their interactions were successfully validated in the Inner Mongolian cohort, in which the five bacterial markers distinguished GC from SG with an AUC of 0.81. Conclusions In addition to microbial compositional changes, we identified differences in bacterial interactions across stages of gastric carcinogenesis. The significant enrichments and network centralities suggest potentially important roles of P. stomatis, D. pneumosintes, S. exigua, P. micra and S. anginosus in GC progression.
Towards a universal neural network encoder for time series

We study the use of a time series encoder to learn representations that are useful on data set types with which it has not been trained on. The encoder is formed of a convolutional neural network whose temporal output is summarized by a convolutional attention mechanism. This way, we obtain a compact, fixed-length representation from longer, variable-length time series. We evaluate the performance of the proposed approach on a well-known time series classification benchmark, considering full adaptation, partial adaptation, and no adaptation of the encoder to the new data type. Results show that such strategies are competitive with the state-of-the-art, often outperforming conceptually-matching approaches. Besides accuracy scores, the facility of adaptation and the efficiency of pre-trained encoders make them an appealing option for the processing of scarcely- or non-labeled time series.
A Novel Assessment and Profiling of Multidimensional Apathy in Alzheimer's Disease.

BACKGROUND Apathy is a complex multidimensional syndrome frequently reported in Alzheimer's disease (AD) and is associated with impaired awareness. Here we present a psychometrically robust method to profile apathy in AD. OBJECTIVES To determine the validity and reliability of a multidimensional apathy measure, the Dimensional Apathy Scale (DAS), and explore the apathy subtype profile and its associations in AD. METHODS 102 people with AD and 55 healthy controls were recruited. Participants completed the DAS, the Apathy Evaluation Scale (AES), Geriatric Depression Short form (GDS-15), and Lawton Instrumental Activities of Daily Living (LIADL). Psychometric properties of the DAS were determined. AD-Control comparison was performed to explore group differences on the DAS. Latent Class Analysis (LCA) was used to explore the profile of apathy in AD. RESULTS The DAS had a good to excellent Cronbach's standardized alpha (self-rated = 0.85, informant/carer-rated = 0.93) and good convergent and divergent validity against standard apathy (AES) and depression (GDS-15) measures. Group comparison showed people with AD were significantly higher for all apathy subtypes than controls (p < 0.001), and lacking in awareness over all apathy subtype deficits. LCA showed three distinct AD subgroups, with 42.2% in the Executive-Initiation apathy, 28.4% in the Global apathy, and 29.4% in the Minimal apathy group. CONCLUSIONS The DAS is a psychometrically robust method of assessing multidimensional apathy in AD. The apathy profiles in AD are heterogeneous, with additional specific impairments relating to awareness dependent on apathy subtype.
hyperdoc2vec: Distributed Representations of Hypertext Documents

Hypertext documents, such as web pages and academic papers, are of great importance in delivering information in our daily life. Although being effective on plain documents, conventional text embedding methods suffer from information loss if directly adapted to hyper-documents. In this paper, we propose a general embedding approach for hyper-documents, namely, hyperdoc2vec, along with four criteria characterizing necessary information that hyper-document embedding models should preserve. Systematic comparisons are conducted between hyperdoc2vec and several competitors on two tasks, i.e., paper classification and citation recommendation, in the academic paper domain. Analyses and experiments both validate the superiority of hyperdoc2vec to other models w.r. t. the four criteria.
Species differences in cannabinoid receptor 2 (CNR2 gene): identification of novel human and rodent CB2 isoforms, differential tissue expression and regulation by cannabinoid receptor ligands

Cannabinoids, endocannabinoids and marijuana activate two well‐characterized cannabinoid receptors (CB‐Rs), CB1‐Rs and CB2‐Rs. The expression of CB1‐Rs in the brain and periphery has been well studied, but neuronal CB2‐Rs have received much less attention than CB1‐Rs. Many studies have now identified and characterized functional glial and neuronal CB2‐Rs in the central nervous system. However, many features of CB2‐R gene structure, regulation and variation remain poorly characterized in comparison with the CB1‐R. In this study, we report on the discovery of a novel human CB2 gene promoter transcribing testis (CB2A) isoform with starting exon located ca 45 kb upstream from the previously identified promoter transcribing the spleen isoform (CB2B). The 5′ exons of both CB2 isoforms are untranslated 5′UTRs and alternatively spliced to the major protein coding exon of the CB2 gene. CB2A is expressed higher in testis and brain than CB2B that is expressed higher in other peripheral tissues than CB2A. Species comparison found that the CB2 gene of human, rat and mouse genomes deviated in their gene structures and isoform expression patterns. mCB2A expression was increased significantly in the cerebellum of mice treated with the CB‐R mixed agonist, WIN55212‐2. These results provide much improved information about CB2 gene structure and its human and rodent variants that should be considered in developing CB2‐R‐based therapeutic agents.
Are allergic multimorbidities and IgE polysensitization associated with the persistence or re‐occurrence of foetal type 2 signalling? The MeDALL hypothesis

Allergic diseases [asthma, rhinitis and atopic dermatitis (AD)] are complex. They are associated with allergen‐specific IgE and nonallergic mechanisms that may coexist in the same patient. In addition, these diseases tend to cluster and patients present concomitant or consecutive diseases (multimorbidity). IgE sensitization should be considered as a quantitative trait. Important clinical and immunological differences exist between mono‐ and polysensitized subjects. Multimorbidities of allergic diseases share common causal mechanisms that are only partly IgE‐mediated. Persistence of allergic diseases over time is associated with multimorbidity and/or IgE polysensitization. The importance of the family history of allergy may decrease with age. This review puts forward the hypothesis that allergic multimorbidities and IgE polysensitization are associated and related to the persistence or re‐occurrence of foetal type 2 signalling. Asthma, rhinitis and AD are manifestations of a common systemic immune imbalance (mesodermal origin) with specific patterns of remodelling (ectodermal or endodermal origin). This study proposes a new classification of IgE‐mediated allergic diseases that allows the definition of novel phenotypes to (i) better understand genetic and epigenetic mechanisms, (ii) better stratify allergic preschool children for prognosis and (iii) propose novel strategies of treatment and prevention.
Epidemiological evaluation of Leishmania infantum zoonotic transmission risk in the recently established endemic area of Northwestern Italy

Leishmania infantum infection had been expanding into new areas due to changes in vector and host biology. Zoonotic visceral leishmaniasis has become endemic in previously unsuitable areas as vectors find favourable climatic conditions and an increasing number of reservoir dogs are moved between traditionally and new endemic areas. Monitoring vector and disease expansion in areas of recent colonization is needed to understand transmission mechanisms and patterns of disease establishment. Here, we studied the infection status of 815 human blood donors and of 803 sympatric dogs from five, newly endemic, areas in Northwestern Italy. In autochthonous dogs, the seroprevalence of anti‐L. infantum antibodies, recorded by Western blot, reached 42.22%, while in humans, the seroprevalence was of 16.81%. No significant correlation between the infection status of dogs and that of their human owners was found, but L. infantum infection was recorded in the different study areas with significant levels of diversity. Restriction fragment length polymorphism showed a high genetic variability of the circulating strains and gave useful insights on patterns of disease establishment into a naïve area.
Models of the electrically stimulated binaural system: A review

ABSTRACT In an increasing number of countries, the standard treatment for deaf individuals is moving toward the implantation of two cochlear implants. Today’s device technology and fitting procedure, however, appears as if the two implants would serve two independent ears and brains. Many experimental studies have demonstrated that after careful matching and balancing of left and right stimulation in controlled laboratory studies most patients have almost normal sensitivity to interaural level differences and some sensitivity to interaural time differences (ITDs). Mechanisms underlying the limited ITD sensitivity are still poorly understood and many different aspects may contribute. Recent pioneering computational approaches identified some of the functional implications the electric input imposes on the neural brainstem circuits. Simultaneously these studies have raised new questions and certainly demonstrated that further refinement of the model stages is necessary. They join the experimental study’s conclusions that binaural device technology, binaural fitting, specific speech coding strategies, and binaural signal processing algorithms are obviously missing components to maximize the benefit of bilateral implantation. Within this review, the existing models of the electrically stimulated binaural system are explained, compared, and discussed from a viewpoint of a “CI device with auditory system” and from that of neurophysiological research.
Congenital Microphthalmos With Orbital Cysts: Distinct Diagnostic Features and Management

Purpose: To review the clinical features and treatment strategies for microphthalmic globes with orbital cyst. Methods: The clinical records of 23 patients treated for microphthalmos associated with orbital cysts were reviewed retrospectively. Results: Most cases of congenital microphthalmos with orbital cysts were first noted at birth, and all were confirmed by means of computed tomography and/or ultrasonography. Six of the 23 cases were bilateral. Sixty-seven percent of bilateral and 29% of unilateral cases also had other congenital malformations. Mild microphthalmos was noted in 3 orbits, moderate in 16 orbits, and severe in 10 orbits. On the basis of clinical findings, 8 orbits were treated with enucleation and cyst excision and 15 were treated with cyst excision only. Cyst aspiration was performed on 5 orbits; 2 required aspiration and subsequent cyst excision. Twenty-six orbits had good cosmesis and 2 had acceptable cosmesis. The mean follow-up interval was 5.15 years. Conclusions: Management of microphthalmos with orbital cyst is a cosmetic issue. Cyst size, degree of microphthalmos, and general condition of the patient determine the best treatment approach.
Prevalence of Opisthorchis viverrini infection and incidence of cholangiocarcinoma in Khon Kaen, Northeast Thailand

Liver cancer is the most common cancer in Khon Kaen, Northeast Thailand, because of the high incidence of cholangiocarcinoma (CHCA). Opisthorchis viverrini (OV), a liver fluke, is endemic in the area, and has been evaluated as a cause of CHCA by International Agency for Research on Cancer. Residents of 20 districts in the province were invited to attend a mobile screening programme between 1990 and 2001. Of 24 723 participants, 18 393 aged 35–69 years were tested for OV infection, by examining stools for the presence of eggs. Prevalence of infection in each district was estimated from the sample of the population who had been tested. The incidence of liver cancer in 1990–2001 was obtained for each district from the cancer registry. The average crude prevalence of OV infection in the sample subjects was 24.5%, ranging from 2.1% to 70.8% in different districts. Truncated age‐standardized incidence of CHCA at ages >35 years varied threefold between districts, from 93.8 to 317.6 per 100 000 person‐years. After adjustment for age group, sex and period of sampling, there was a positive association between prevalence of OV infection and incidence of CHCA at the population level. Associations between CHCA and active OV infection in individuals have become hard to demonstrate, because of effective anti‐OV treatment. The relationship may, however, be clear in comparisons between populations, which, for infectious diseases, take into account the contextual effects of group exposure in determining individual outcome. The cancer registry is an appropriate tool for disease monitoring in small areas.
Composite patterns in neutral/neutral two-dimensional gels demonstrate inefficient replication origin usage

The neutral/neutral two-dimensional (2-D) gel replicon mapping technique has been used to great advantage to localize and characterize origins of replication. Interestingly, many yeast origins display a composite pattern consisting of both a bubble arc and a single-fork arc. Moreover, in every instance in which neutral/neutral 2-D gels have been used to analyze origins in higher eukaryotic cells, two or more adjacent fragments display these composite patterns. We believe that composite patterns signal inefficient origin usage in yeast cells because the replicators in question are not active in every cell cycle and in higher eukaryotic replicons because initiation sites are chosen from among many potential sites lying within a zone. However, others have suggested that the single-fork arcs in these composite gel patterns arise from nicking activity that converts replication bubbles to branched structures that comigrate with bona fide single forks. Here, we have used three different replicon mapping strategies to show that broken simian virus 40 replication bubbles trace unique arcs that are clearly distinguishable from classic, intact single forks. Thus, it is likely that composite 2-D gel patterns represent origins that are inefficiently utilized.
Adenosine–cannabinoid receptor interactions. Implications for striatal function

Adenosine and endocannabinoids are very ubiquitous non‐classical neurotransmitters that exert a modulatory role on the transmission of other more ‘classical’ neurotransmitters. In this review we will focus on their common role as modulators of dopamine and glutamate neurotransmission in the striatum, the main input structure of the basal ganglia. We will pay particular attention to the role of adenosine A2A receptors and cannabinoid CB1 receptors. Experimental results suggest that presynaptic CB1 receptors interacting with A2A receptors in cortico‐striatal glutamatergic terminals that make synaptic contact with dynorphinergic medium‐sized spiny neurons (MSNs) are involved in the motor‐depressant and addictive effects of cannabinoids. On the other hand, postsynaptic CB1 receptors interacting with A2A and D2 receptors in the dendritic spines of enkephalinergic MSNs and postsynaptic CB1 receptors in the dendritic spines of dynorphinergic MSN are probably involved in the cataleptogenic effects of cannabinoids. These receptor interactions most probably depend on the existence of a variety of heteromers of A2A, CB1 and D2 receptors in different elements of striatal spine modules. Drugs selective for the different striatal A2A and CB1 receptor heteromers could be used for the treatment of neuropsychiatric disorders and drug addiction and they could provide effective drugs with fewer side effects than currently used drugs.
Roles of Soybean Plasma Membrane Intrinsic Protein GmPIP2;9 in Drought Tolerance and Seed Development

Aquaporins play an essential role in water uptake and transport in vascular plants. The soybean genome contains a total of 22 plasma membrane intrinsic protein (PIP) genes. To identify candidate PIPs important for soybean yield and stress tolerance, we studied the transcript levels of all 22 soybean PIPs. We found that a GmPIP2 subfamily member, GmPIP2;9, was predominately expressed in roots and developing seeds. Here, we show that GmPIP2;9 localized to the plasma membrane and had high water channel activity when expressed in Xenopus oocytes. Using transgenic soybean plants expressing a native GmPIP2;9 promoter driving a GUS-reporter gene, it was found high GUS expression in the roots, in particular, in the endoderm, pericycle, and vascular tissues of the roots of transgenic plants. In addition, GmPIP2;9 was also highly expressed in developing pods. GmPIP2;9 expression significantly increased in short term of polyethylene glycol (PEG)-mediated drought stress treatment. GmPIP2;9 overexpression increased tolerance to drought stress in both solution cultures and soil plots. Drought stress in combination with GmPIP2;9 overexpression increased net CO2 assimilation of photosynthesis, stomata conductance, and transpiration rate, suggesting that GmPIP2;9-overexpressing transgenic plants were less stressed than wild-type (WT) plants. Furthermore, field experiments showed that GmPIP2;9-overexpressing plants had significantly more pod numbers and larger seed sizes than WT plants. In summary, the study demonstrated that GmPIP2;9 has water transport activity. Its relative high expression levels in roots and developing pods are in agreement with the phenotypes of GmPIP2;9-overexpressing plants in drought stress tolerance and seed development.
Mitochondrial Dysfunction and Immune Cell Metabolism in Sepsis

Sepsis is a life threatening condition mediated by systemic infection, but also triggered by hemorrhage and trauma. These are significant causes of organ injury implicated in morbidity and mortality, as well as post-sepsis complications associated with dysfunction of innate and adaptive immunity. The role of cellular bioenergetics and loss of metabolic plasticity of immune cells is increasingly emerging in the pathogenesis of sepsis. This review describes mitochondrial biology and metabolic alterations of immune cells due to sepsis, as well as indicates plausible therapeutic opportunities.
PCSK9: From Basic Science Discoveries to Clinical Trials

Unknown 15 years ago, PCSK9 (proprotein convertase subtilisin/kexin type 9) is now common parlance among scientists and clinicians interested in prevention and treatment of atherosclerotic cardiovascular disease. What makes this story so special is not its recent discovery nor the fact that it uncovered previously unknown biology but rather that these important scientific insights have been translated into an effective medical therapy in record time. Indeed, the translation of this discovery to novel therapeutic serves as one of the best examples of how genetic insights can be leveraged into intelligent target drug discovery. The PCSK9 saga is unfolding quickly but is far from complete. Here, we review major scientific understandings as they relate to the role of PCSK9 in lipoprotein metabolism and atherosclerotic cardiovascular disease and the impact that therapies designed to inhibit its action are having in the clinical setting.
Foot cooling does not improve vigilance but may transiently reduce sleepiness

Temperature of the skin (TSk) and core (TC) play key roles in sleep–wake regulation. The diurnal combination of low TSk and high TC facilitates alertness, whereas the transition to high TSk and low TC correlates with sleepiness. Sleepiness and deteriorating vigilance are induced with peripheral warming, whereas peripheral cooling appears to transiently improve vigilance in narcolepsy. This study aimed to test the hypothesis that foot cooling would maintain vigilance during extended wakefulness in healthy adults. Nine healthy young adult participants with habitually normal sleep completed three constant‐routine trials in randomized crossover order. Trials began at 22:30 hours, and involved continuous mild foot cooling (30°C), moderate foot cooling (25°C) or no foot cooling, while undertaking six × 10‐min Psychomotor Vigilance Tasks and seven × 7‐min Karolinska Drowsiness Tasks, interspersed with questionnaires of sleepiness and thermal perceptions. Foot temperatures in control, mild and moderate cooling averaged 34.5 ± 0.5°C, 30.8 ± 0.2°C and 26.4 ± 0.1°C (all p < .01), while upper‐limb temperatures remained stable (34–35°C) and TC declined (approximately −0.12°C per hr) regardless of trial (p = .84). Foot cooling did not improve vigilance (repeated‐measures‐ANOVA interaction for response speed: p = .45), but transiently reduced subjective sleepiness (−0.8 ± 0.8; p = .004). Participants felt cooler throughout cooling trials, but thermal comfort was unaffected (p = .43), as were almost all Karolinska Drowsiness Tasks’ encephalographic parameters. In conclusion, mild or moderate cooling of the feet did not attenuate declines in vigilance or core temperature of healthy young adults during the period of normal sleep onset and early sleep, and any effect on sleepiness was small and transient.
Cremona transformations and derived equivalences of K3 surfaces

We exhibit a Cremona transformation of $\mathbb{P}^{4}$ such that the base loci of the map and its inverse are birational to K3 surfaces. The two K3 surfaces are derived equivalent but not isomorphic to each other. As an application, we show that the difference of the two K3 surfaces annihilates the class of the affine line in the Grothendieck ring of varieties.
13. Figurative phraseology and culture

This chapter seeks to outline the main trends in research on cultural aspects of conventional figurative language (phraseology in particular) and to describe the connection between figurative units (such as idioms, proverbs, etc.) and culture as it becomes manifest in phraseological data from several languages. Numerous studies have highlighted the fact that phrasemes are not only units of a sign system, language, but also carriers of cultures, pointing out the necessity for modern phraseological research to turn to cultural phenomena. What exactly constitutes the connection between figurative phrasemes and culture, however, has never been examined systematically. This chapter uses a typology of the cultural phenomena which underlie phrasemes, along with the relevant phraseological types, to explore this connection. In doing so, one has to consider both the literal and the figurative readings of phrasemes, as well as the different levels of describing phrasemes, since there are various ways in which the cultural aspects may become manifest.