Miracle-dz/UniFAR-FTUs huggingface dataset:
Linking the gut microbiota to human health

The human gut is the natural environment for a diverse and dynamic microbial ecosystem, whose structure and functions are presently a major target of research in biomedicine. Experimental studies in germ-free animals performed some decades ago revealed the importance of these microbial communities for normal growth and development and for the maintenance of health in adult life. The host provides habitat and nutrition to the microbial communities and derives many benefits from its symbionts that contribute to metabolic, defensive and trophic functions. Development of novel gene sequencing technologies as well as availability of powerful bioinformatic analysis tools provide new insights into the composition and structure of the human gut microbiota. There is no clear definition of the characteristics of a normal ‘healthy’ gut microbiota in human subjects, but several disease states have been associated with changes in the composition of faecal and intestinal mucosal communities, including inflammatory bowel diseases, obesity and the metabolic syndrome. Probiotics and prebiotics are used to improve symbiosis between enteric microbiota and the host or restore states of dysbiosis.
Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf

Cultivated rice (Oryza sativa L.) is very sensitive to salt stress. So far a few rice landraces have been identified as a source of salt tolerance and utilized in rice improvement. These tolerant lines primarily use Na+ exclusion mechanism in root which removes Na+ from the xylem stream by membrane Na+ and K+ transporters, and resulted in low Na+ accumulation in shoot. Identification of a new donor source conferring high salt tolerance is imperative. Wild relatives of rice having wide genetic diversity are regarded as a potential source for crop improvement. However, they have been less exploited against salt stress. Here, we simultaneously evaluated all 22 wild Oryza species along with the cultivated tolerant lines including Pokkali, Nona Bokra, and FL478, and sensitive check varieties under high salinity (240 mM NaCl). Based on the visual salt injury score, three species (O. alta, O. latifolia, and O. coarctata) and four species (O. rhizomatis, O. eichingeri, O. minuta, and O. grandiglumis) showed higher and similar level of tolerance compared to the tolerant checks, respectively. All three CCDD genome species exhibited salt tolerance, suggesting that the CCDD genome might possess the common genetic factors for salt tolerance. Physiological and biochemical experiments were conducted using the newly isolated tolerant species together with checks under 180 mM NaCl. Interestingly, all wild species showed high Na+ concentration in shoot and low concentration in root unlike the tolerant checks. In addition, the wild-tolerant accessions showed a tendency of a high tissue tolerance in leaf, low malondialdehyde level in shoot, and high retention of chlorophyll in the young leaves. These results suggest that the wild species employ tissue tolerance mechanism to manage salt stress. Gene expression analyses of the key salt tolerance-related genes suggested that high Na+ in leaf of wild species might be affected by OsHKT1;4-mediated Na+ exclusion in leaf and the following Na+ sequestration in leaf might be occurring independent of tonoplast-localized OsNHX1. The newly isolated wild rice accessions will be valuable materials for both rice improvement to salinity stress and the study of salt tolerance mechanism in plants.
Energy Efficiency of SISO and MISO in Visible Light Communication Systems

In this paper, we focus on maximizing energy efficiency problems for visible light communication (VLC) systems. Specifically, for single-input-single-output (SISO) VLC systems, we first systematically analyze the power consumption along the signal processing path and propose an explicit energy efficiency expression, which is a quasi-concave function of the power consumption at the power amplifier (PA). Then, we investigate the energy efficiency maximization problem under both the power constraint and rate requirement. By exploiting Dinkelbach's algorithm and Lagrangian method, the optimal power consumption of PA is obtained in a closed form. Numerical results are presented to evaluate the performance of the proposed optimal solution. Moreover, we analyze the power consumption of multi-LED and study the energy efficiency maximization problem for the multi-input-single-output (MISO) VLC system, under both per LED's power constraint and rate constraint. This problem is shown to be nonconvex. With leveraging Dinkelbach's algorithm, the original problem can be reformulated as a convex problem, and the optimal solution can be efficiently obtained by the interior point algorithm. Meanwhile, numerical results are presented to show the performance of the proposed optimal solutions. In particular, it is shown that the power is preferentially allocated to the subchannels with higher channel gain in the MISO VLC system.
Organ-selective growth in the offspring of protein-restricted mothers

Recent epidemiological studies in people whose birth weights were recorded many years ago suggest links between impaired growth during early life and the development of diseases, including diabetes, much later in life. The long-term effects of retarded early growth are proposed to result from malnutrition at critical periods of fetal or infant development leading to reduction in the growth of organs and permanent changes in their metabolism or structure, or both. In order to investigate this, a rat model was established which involved feeding either a diet containing 200 g protein/kg or an isoenergetic diet containing 80 g protein/kg to pregnant and lactating rats. In addition, cross-fostering techniques were employed which allowed a separate evaluation of the prenatal or the postnatal periods. The offspring were studied at 21 d of age or were weaned onto a normal laboratory chow and studied at 11 months of age. The 80g protein/kg diet during pregnancy did not affect the overall reproductive performance although more subtle differences were evident. Permanent growth retardation was evident in offspring subjected to maternal protein restriction during the postnatal period. At 21 d of age the offspring of protein-restricted mothers exhibited selective changes in organ growth: compared with the body weight, the lung and brain experienced a smaller decrease in weight; the heart, kidney and thymus decreased proportionately; whereas, the pancreas, spleen, muscle and liver showed a greater reduction in weight. In older animals the muscle weight was lower in the male rats and the relative weight ofpancreas was increased in the female rats.
Assessment and interpretation of micronutrient status during pregnancy

Accurate assessment of maternal micronutrient status is critical to the prevention of suboptimal micronutrient status and anaemia during pregnancy. Measurement of Fe, folate and vitamin B12 status is complicated by adaptive changes to maternal and placental physiology that markedly affect concentrations of circulating micronutrients and their functional biomarkers. Validation of new assessment methods by comparison with gold standards is often prevented by ethical considerations. Antenatal screening in the UK is predominantly concerned with the detection of anaemia, although estimation of maternal Fe stores by serum ferritin at the start of antenatal care may be a more effective preventive strategy. Functional assessment of maternal anaemia is highly problematic, so instead reference data are used for its definition. The effect of mild-to-moderate anaemia on pregnancy outcome is unclear because of the crude nature of its assessment and the influence of confounding factors. Fe-deficient erythropoiesis may be detected by assessment of erythrocyte Zn protoporphyrin and reticulocyte Hb, although such measures may be unavailable in many clinical laboratories. Serum soluble transferrin receptor is highly responsive to tissue Fe deficiency and is less affected by inflammation than most other indicators. Direct inter-assay comparison of serum and erythrocyte folate values is inadvisable since recovery rates differ greatly between methods. Serum total homocysteine is a useful functional biomarker of both folate and vitamin B12 status but during pregnancy is influenced by other factors that reduce its sensitivity. Isotope-dilution liquid chromatography–tandem MS and serum holo-transcobalamin provide new opportunities to gain detailed data of folate species and vitamin B12 fractions in large samples.
High performance polyethylene nanocomposite fibers

A high density polyethylene (HDPE) matrix was melt compounded with 2 vol% of dimethyldichlorosilane treated fumed silica nanoparticles. Nanocomposite fibers were prepared by melt spinning through a co-rotating twin screw extruder and drawing at 125°C in air. Thermo-mechanical and morphological properties of the resulting fibers were then investigated. The introduction of nanosilica improved the drawability of the fibers, allowing the achievement of higher draw ratios with respect to the neat matrix. The elastic modulus and creep stability of the fibers were remarkably improved upon nanofiller addition, with a retention of the pristine tensile properties at break. Transmission electronic microscope (TEM) images evidenced that the original morphology of the silica aggregates was disrupted by the applied drawing.
Immune Escape Mechanisms and Future Prospects for Immunotherapy in Neuroblastoma

Neuroblastoma (NB) is the most common extracranial solid tumor in childhood with 5-year survival rate of 40% in high-risk patients despite intensive therapies. Recently, adoptive cell therapy, particularly chimeric antigen receptor (CAR) T cell therapy, represents a revolutionary treatment for hematological malignancies. However, there are challenges for this therapeutic strategy with solid tumors, as a result of the immunosuppressive nature of the tumor microenvironment (TME). Cancer cells have evolved multiple mechanisms to escape immune recognition or to modulate immune cell function. Several subtypes of immune cells that infiltrate tumors can foster tumor development, harbor immunosuppressive activity, and decrease an efficacy of adoptive cell therapies. Therefore, an understanding of the dual role of the immune system under the influences of the TME has been crucial for the development of effective therapeutic strategies against solid cancers. This review aims to depict key immune players and cellular pathways involved in the dynamic interplay between the TME and the immune system and also to address challenges and prospective development of adoptive T cell transfer for neuroblastoma.
Root navigation by self inhibition

Circumventing physical obstacles is critical for a plant's survival and performance. Although the ability of roots to circumvent obstacles has been known for over 100 years, the phenomena and its mechanisms have received relatively little attention. In this study it is demonstrated that roots of Pisum sativum are able to detect and avoid growth towards inanimate obstacles and the hypothesis that this behaviour is based on the sensitivity of roots to their own allelopathic exudates that accumulate in the vicinity of physical obstacles is tested. The development of lateral roots of Pisum sativum towards an obstacle (a piece of nylon string, similar in dimensions to a plant root) was followed. Lateral roots were similar in number, but significantly shorter in the direction of the nylon string. In addition, up to half of the lateral roots that developed towards the nylon string withered, whereas no withering was observed in the absence of the nylon string. These avoidance growth patterns were suppressed in the presence of potassium permanganate or activated carbon, indicating a role of allelopathic exudates in promoting obstacle avoidance. The demonstrated obstacle avoidance by self inhibition could increase plant performance by limiting resource allocation to less promising parts of the root system.
Agreement Analysis: What He Said, She Said Versus You Said

Correlation and agreement are 2 concepts that are widely applied in the medical literature and clinical practice to assess for the presence and strength of an association. However, because correlation and agreement are conceptually distinct, they require the use of different statistics. Agreement is a concept that is closely related to but fundamentally different from and often confused with correlation. The idea of agreement refers to the notion of reproducibility of clinical evaluations or biomedical measurements. The intraclass correlation coefficient is a commonly applied measure of agreement for continuous data. The intraclass correlation coefficient can be validly applied specifically to assess intrarater reliability and interrater reliability. As its name implies, the Lin concordance correlation coefficient is another measure of agreement or concordance. In undertaking a comparison of a new measurement technique with an established one, it is necessary to determine whether they agree sufficiently for the new to replace the old. Bland and Altman demonstrated that using a correlation coefficient is not appropriate for assessing the interchangeability of 2 such measurement methods. They in turn described an alternative approach, the since widely applied graphical Bland–Altman Plot, which is based on a simple estimation of the mean and standard deviation of differences between measurements by the 2 methods. In reading a medical journal article that includes the interpretation of diagnostic tests and application of diagnostic criteria, attention is conventionally focused on aspects like sensitivity, specificity, predictive values, and likelihood ratios. However, if the clinicians who interpret the test cannot agree on its interpretation and resulting typically dichotomous or binary diagnosis, the test results will be of little practical use. Such agreement between observers (interobserver agreement) about a dichotomous or binary variable is often reported as the kappa statistic. Assessing the interrater agreement between observers, in the case of ordinal variables and data, also has important biomedical applicability. Typically, this situation calls for use of the Cohen weighted kappa. Questionnaires, psychometric scales, and diagnostic tests are widespread and increasingly used by not only researchers but also clinicians in their daily practice. It is essential that these questionnaires, scales, and diagnostic tests have a high degree of agreement between observers. It is therefore vital that biomedical researchers and clinicians apply the appropriate statistical measures of agreement to assess the reproducibility and quality of these measurement instruments and decision-making processes.
Complex activities of daily living vary by mild cognitive impairment subtype

Abstract There is increasing consensus regarding the importance of operationally defining and measuring functional decline in mild cognitive impairment (MCI). However, few studies have directly examined functional abilities in MCI or its presumed subtypes and, to date, reported findings have been discrepant. Nondemented older adults (n = 120) were administered a comprehensive cognitive battery measuring multiple domains as well as a performance-based functional ability measure. Participants were characterized as either cognitively normal, amnestic MCI, or non-amnestic MCI. MCI individuals demonstrated decrements in instrumental activities of daily living (IADL) relative to their cognitively normal counterparts. Specifically, participants with amnestic MCI demonstrated significant decrements in financial management, whereas those with non-amnestic MCI showed poorer performance in abilities related to health and safety. Moreover, decreased functional abilities were associated with decrements in global cognitive functioning but not memory or executive functions in the MCI participants. Finally, logistic regression demonstrated that functional abilities accurately predicted MCI subtype. Results support the need for better delineation of functional decline in MCI. Given the implications of functional status for MCI diagnosis and treatment, the direct assessment of functional abilities is recommended. Results further suggest performance-based IADL assessment may have utility in distinguishing MCI subtypes. (JINS, 2010, 16, 630–639.)
Artemisia Extract Suppresses NLRP3 and AIM2 Inflammasome Activation by Inhibition of ASC Phosphorylation

Artemisia princeps var. orientalis (Asteraceae, A. princeps) is a well-known traditional medicinal herb used for treating various inflammatory disorders in Korea, Japan, China, and other Asian countries. In the present study, we investigated the effects of A. princeps extract (APO) on interleukin- (IL-) 1β regulation and inflammasome activation in bone marrow-derived macrophages (BMDMs) and monosodium urate- (MSU-) induced peritonitis mouse model in vivo. The APO treatment to BMDMs primed with lipopolysaccharide (LPS) attenuated the NLRP3 and AIM2 inflammasome activation induced by danger signals, such as ATP, nigericin, silica crystals, and poly (dA:dT), respectively. Mechanistic study revealed that APO suppressed the ASC oligomerization and speck formation, which are required for inflammasome activation. APO treatment also reduced the ASC phosphorylation induced by the combination of LPS and a tyrosine phosphatase inhibitor. In vivo evaluation revealed that intraperitoneal administration of APO reduced IL-1β levels, significantly (p < 0.05) and dose dependently, in the MSU-induced peritonitis mouse model. In conclusion, our study is the first to report that the extract of A. princeps inhibits inflammasome activation through the modulation of ASC phosphorylation. Therefore, APO might be developed as therapeutic potential in the treatment of inflammasome-mediated inflammatory disorders, such as gouty arthritis.
Plague as a biological weapon: medical and public health management. Working Group on Civilian Biodefense.

OBJECTIVE The Working Group on Civilian Biodefense has developed consensus-based recommendations for measures to be taken by medical and public health professionals following the use of plague as a biological weapon against a civilian population. PARTICIPANTS The working group included 25 representatives from major academic medical centers and research, government, military, public health, and emergency management institutions and agencies. EVIDENCE MEDLINE databases were searched from January 1966 to June 1998 for the Medical Subject Headings plague, Yersinia pestis, biological weapon, biological terrorism, biological warfare, and biowarfare. Review of the bibliographies of the references identified by this search led to subsequent identification of relevant references published prior to 1966. In addition, participants identified other unpublished references and sources. Additional MEDLINE searches were conducted through January 2000. CONSENSUS PROCESS The first draft of the consensus statement was a synthesis of information obtained in the formal evidence-gathering process. The working group was convened to review drafts of the document in October 1998 and May 1999. The final statement incorporates all relevant evidence obtained by the literature search in conjunction with final consensus recommendations supported by all working group members. CONCLUSIONS An aerosolized plague weapon could cause fever, cough, chest pain, and hemoptysis with signs consistent with severe pneumonia 1 to 6 days after exposure. Rapid evolution of disease would occur in the 2 to 4 days after symptom onset and would lead to septic shock with high mortality without early treatment. Early treatment and prophylaxis with streptomycin or gentamicin or the tetracycline or fluoroquinolone classes of antimicrobials would be advised.
The (cid:1) 2 -Adrenoceptor Agonist Dexmedetomidine Converges on an Endogenous Sleep-promoting Pathway to Exert Its Sedative Effects

Background: The authors investigated whether the sedative, or hypnotic, action of the general anesthetic dexmedetomidine (a selective (cid:1) 2 -adrenoceptor agonist) activates endogenous non- rapid eye movement (NREM) sleep-promoting pathways. Methods: c-Fos expression in sleep-promoting brain nuclei was assessed in rats using immunohistochemistry and in situ hybridization. Next, the authors perturbed these pathways us- ing (1) discrete lesions induced by ibotenic acid, (2) local and systemic administration of (cid:2) -aminobutyric acid receptor type A (GABA A ) receptor antagonist gabazine, or (3) (cid:1) 2 -adrenoceptor antagonist atipamezole in rats, and (4) genetic mutation of the (cid:1) 2A -adrenoceptor in mice. Results: Dexmedetomidine induced a qualitatively similar pattern of c-Fos expression in rats as seen during normal NREM sleep, i.e. , a decrease in the locus ceruleus (LC) and tuberomammillary nucleus (TMN) and an increase in the ventrolateral preoptic nucleus (VLPO). These changes were attenuated by atipamezole and were not seen in mice lacking functional (cid:1) 2A - adrenoceptors, which do not Conclusions: The authors propose that endogenous sleep pathways are causally involved in dexmedetomidine-induced sedation; dexmedetomidine’s sedative mechanism involves in- hibition of the LC, which disinhibits VLPO ﬁring. The increased release of GABA at the terminals of the VLPO inhibits TMN ﬁring, which is required for the sedative response.
On Probability of Detection Lossless Concurrent Error Detection Based on Implications

In recent years, a new concurrent error detection method by using invariant relationships inside a circuit, called implications, has been proposed. Algorithms have also been developed to reduce the total number of required implications so as to minimize the incurred area overhead due to implication checking logic. This implication reduction process, however, would result in degradation on the probability of error detection (<inline-formula> <tex-math notation="LaTeX">${P}_{{\mathrm{ detection}}}$ </tex-math></inline-formula>) of the method. In this paper, we analyze the impact of this issue mathematically together with illustration by a real case study. Our analytical results show that just one percent degradation on <inline-formula> <tex-math notation="LaTeX">${P}_{{\mathrm{ detection}}}$ </tex-math></inline-formula> would result in millions more errors being undetected per second and thereby significant loss on reliability of the target circuit. To address this issue, we develop a new implication reduction algorithm that guarantees no loss on <inline-formula> <tex-math notation="LaTeX">${P}_{{\mathrm{ detection}}}$ </tex-math></inline-formula>. In our algorithm, the detectability of errors for each candidate implication is carefully evaluated. The evaluation results are then utilized to select the most efficient candidates for detecting all the detectable errors. We also analyze the computation and memory complexity of the proposed algorithm. The experimental results on 28 representative benchmark circuits from ISCAS’85, ISCAS’89, and ITC’99 show that the implication reduction rate of our method (92.59%) is close to that of the previous work (95.8%). Only a small number of additional implications need to be selected to guarantee no loss on <inline-formula> <tex-math notation="LaTeX">${P}_{{\mathrm{ detection}}}$ </tex-math></inline-formula>.