Miracle-dz/UniFAR-FTUs huggingface dataset:
Abrupt burial imparts persistent changes to the bacterial diversity of turbidite‐associated sediment profiles

The emplacement of subaqueous gravity‐driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical and biological signatures of turbidite deposition, the response of bacteria and archaea within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and those attached to allochthonous material must respond to substantially altered environmental conditions and selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine (i) the microbial community response to rapid sedimentation and (ii) the preservation and identification of displaced micro‐organisms. We collected Illumina MiSeq sequence libraries across turbidite boundaries at ~26 cm sediment depth in La Jolla Canyon off the coast of California, and at ~50 cm depth in meromictic Twin Lake, Hennepin County, MN. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, both the marine and lacustrine turbidite boundaries are sharply demarcated by the abundance and diversity of Chloroflexi, suggesting a characteristic sensitivity to sediment disturbance history or to differences in organic substrates across turbidite profiles. Variations in the abundance of putative dissimilatory sulfate‐reducing Deltaproteobacteria across the buried La Jolla Canyon sediment–water interface reflect turbidite‐induced changes to the geochemical environment. Species‐level distinctions within the Deltaproteobacteria clearly conform to the sedimentological boundary, suggesting a continuing impact of genetic inheritance distinguishable from broader trends attributable to selective pressure. Abrupt, <1‐cm scale changes in bacterial diversity across the Twin Lake turbidite contact are consistent with previous studies showing that relict DNA signatures attributable to sediment transport may be more easily preserved in low‐energy, anoxic environments. This work raises the possibility that deep subsurface microbial communities may inherit variations in microbial diversity from sediment flow and deformation events.
CSF AND PLASMA SOMATOSTATIN LEVELS IN ACROMEGALY

Cerebrospinal fluid (CSF) and plasma levels of somatostatin have been measured in patients with active acromegaly and the results compared to those obtained in patients with non‐endocrine diseases. Plasma levels have also been studied in acromegalics given oral glucose. The mean CSF somatostatin level in twenty patients without endocrine disease was 76 pg/ml (range 46–112) which did not diner significantly from that found in eight acromegalics (mean 87 pg/ml, range 48–160). Plasma somatostatin in twenty‐two acromegalic patients on no medical treatment was 43 pg/ml (range 9–113), not significantly different from values in a normal control population. There were no differences in the somatostatin levels of non‐diabetic acromegalics. After oral glucose, there was a rise in circulating somatostatin in eleven out of twelve acromegalic patients, and this rise did not differ from that seen in normal subjects. It is probable that altered somatostatin secretion is neither the cause nor the result of acromegaly; however it is possible that local changes in somatostatin concentration which are not reflected in peripheral plasma or CSF levels may occur near the site of its production.
Determinants of the streptococcal surface glycoprotein GspB that facilitate export by the accessory Sec system

GspB is a large cell‐surface glycoprotein expressed by Streptococcus gordonii M99 that mediates binding of this organism to human platelets. This adhesin is glycosylated in the cytoplasm, and is then transported to the cell surface via an accessory Sec system. To assess the structural features of GspB that are needed for export, we examined the effects of altering the carbohydrate moieties or the polypeptide backbone of GspB. Truncated, glycosylated variants of GspB were exported exclusively via the accessory Sec pathway. When glycosylation was abolished, the GspB variants were still exported by this pathway, but minor amounts could also be transported by the canonical Sec system. GspB variants with in‐frame insertions or deletions in the N‐terminus were not secreted, indicating that this domain is necessary for export. However, the N‐terminus is not sufficient for the transport of heterologous proteins, because C‐terminal fusion of passenger proteins to this domain hindered export. In contrast, fusion of GspB to a canonical signal peptide resulted in the efficient export of non‐glycosylated forms of the fusion protein via the canonical Sec pathway, whereas glycosylated forms could not be exported. Thus, the carbohydrate moieties and the atypical signal sequence of GspB interfere with export via the canonical pathway, and direct GspB towards the accessory Sec system.
Endo-β-N-acetylglucosaminidases from Infant Gut-associated Bifidobacteria Release Complex N-glycans from Human Milk Glycoproteins*

Breastfeeding is one of the main factors guiding the composition of the infant gut microbiota in the first months of life. This process is shaped in part by the high amounts of human milk oligosaccharides that serve as a carbon source for saccharolytic bacteria such as Bifidobacterium species. Infant-borne bifidobacteria have developed various molecular strategies for utilizing these oligosaccharides as a carbon source. We hypothesized that these species also interact with N-glycans found in host glycoproteins that are structurally similar to free oligosaccharides in human milk. Endo-β-N-acetylglucosaminidases were identified in certain isolates of Bifidobacterium longum subsp. longum, B. longum subsp. infantis, and Bifidobacterium breve, and their presence correlated with the ability of these strains to deglycosylate glycoproteins. An endoglycosidase from B. infantis ATCC 15697, EndoBI-1, was active toward all major types of N-linked glycans found in glycosylated proteins. Its activity was not affected by core fucosylation or extensive fucosylation, antenna number, or sialylation, releasing several N-glycans from human lactoferrin and immunoglobulins A and G. Extensive N-deglycosylation of whole breast milk was also observed after coincubation with this enzyme. Mutation of the active site of EndoBI-1 did not abolish binding to N-glycosylated proteins, and this mutant specifically recognized Man3GlcNAc2(α1–6Fuc), the core structure of human N-glycans. EndoBI-1 is constitutively expressed in B. infantis, and incubation of the bacterium with human or bovine lactoferrin led to the induction of genes associated to import and consumption of human milk oligosaccharides, suggesting linked regulatory mechanisms among these glycans. This work reveals an unprecedented interaction of bifidobacteria with host N-glycans and describes a novel endoglycosidase with broad specificity on diverse N-glycan types, potentially a useful tool for glycoproteomics studies.
Beyond geometries of activity spaces: A holistic study of daily travel patterns, individual characteristics, and perceived wellbeing in Helsinki metropolitan area

Activity space (AS) is a measure of spatial behavior used to summarize the mobility behavior of individuals. Current studies often highlight the fact that AS is highly complex and multidimensional in character. Therefore, the need for more holistic approaches providing more comprehensive descriptions of mobility patterns is evident. This article assesses the activity spaces of young adults aged 25–40 living in the Helsinki metropolitan area using a dataset collected with an online map survey. Using a wide range of measurements covering different aspects of AS, we identified seven components that define activity spaces, namely size, intensity of activities, volume of trips, exteriority, polycentricity, elongation, and destination specialization. We then used the components together with travel mode use to identify a typology of daily mobility patterns. The results show that individuals with different types of AS differ significantly in their socio-demographic characteristics, such as age, gender, employment, household characteristics, and residential neighborhood. Furthermore, the study reveals interesting associations between AS characteristics and different aspects of wellbeing. Overall, the results highlight the importance of multidimensional and comprehensive approaches to understanding daily mobility of urban residents.
Sensitivity-Based Discrete Coordinate-Descent for Volt/VAr Control in Distribution Networks

The discrete coordinate-descent algorithm is a practical approach that is currently used in centralized Volt/VAr Control (VVC) implementations, mainly due to its good performance and speed for real-time applications. Its viability is however challenged by the increasing number of distributed generation that contribute to the VVC solution, in addition to the conventional transformer taps and switched capacitors. This paper presents the exact computation of sensitivity factors that speed up the discrete coordinate-descent implementation, by significantly reducing the number of forward/backward substitutions in the current injection power flow method; the speed up is achieved without affecting the control setting quality of the original implementation. The optimality of the discrete coordinate-descent solutions is investigated by computing the gaps relative to mixed-integer linear programming set-points, derived from a polyhedral reformulation of the VVC problem. The sensitivity-based discrete coordinate-descent algorithm is tested starting from two initial points, the default one given by the current control set-points, and a continuous solution obtained from a linear approximation of the VVC problem. Numerical results on networks with up to 3145 nodes show that the sensitivity-based approach significantly improves the runtime of the discrete coordinate-descent algorithm, and that the linear programming initialization leads to VVC solutions with gaps relative to the mixed-integer set-points that are less than 0.5%.
Towards an Understanding of Physiological Body Mass Regulation: Seasonal Animal Models

This review is based around a number of interlinked hypotheses that can be summarised as follows: (i) mammalian body mass is regulated, (ii) the mechanisms that effect this regulation are common to all mammalian species, including humans, (iii) the neurochemical substrates involved in long term body mass regulation and in determining the level of body mass that will be defended may not be the same as those involved in short term energy homeostasis, or body mass defence, or may be differentially engaged, and (iv) “appropriate” body mass is encoded somewhere within the mammalian brain and acts as a comparator to influence both nutritional and reproductive physiology. These issues are of direct relevance to the epidemic of obesity in the Westernised human population and the poor success rate of conventional weight loss strategies. It is our contention that seasonal rodent models, and the Siberian hamster in particular, represent extremely valuable tools for the study of the mechanistic basis of body mass regulation. The Siberian hamster model is often perceived as an unusual mammalian variant that has evolved an almost counter-intuitive strategy for surviving periods of anticipated seasonal food shortage. However, there is compelling evidence that these animals are able to adjust their body mass continually and progressively according to their photoperiodic history, i.e. a seasonally-appropriate body mass. These adjustments to appropriate body mass are memorised even after the animals have been driven away from their normal body mass trajectory by imposed food restriction. Thus, photoperiod, acting through the pineal hormone, melatonin, is able to reset the desired body mass for a given time in the seasonal cycle. Importantly, daylength provides a tool to manipulate the body mass control system in an entirely physiological and stress-free manner. While resetting of body mass by photoperiod represents a level of control apparently confined to seasonal mammals, it has the potential to reveal mechanisms of generic importance in the regulation of energy homeostasis.
History and Global Burden of Viral Hepatitis

Between 1963 and 1989, 5 hepatotropic viruses have been discovered that are the major causes of viral hepatitides worldwide: hepatitis A virus, hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis delta virus and hepatitis E virus. Their epidemiology and pathogenesis have been studied in great detail. Furthermore, the structure and genetic organization of their DNA or RNA genome including the viral life cycle have been elucidated and have been successfully translated into important clinical applications, such as the specific diagnosis, therapy and prevention of the associated liver diseases, including liver cirrhosis and hepatocellular carcinoma (HCC). The prevalence of acute and chronic viral hepatitis A-E shows distinct geographic differences. The global burden of disease (prevalence, incidence, death, disability-adjusted life years) has been analyzed in seminal studies that show that the worldwide prevalence of hepatitis A-E has significantly decreased between 1990 and 2013. During the same time, the incidence of HBV-related liver cirrhosis and HCC, respectively, also decreased or increased slightly, the incidence of the HCV-related liver cirrhosis remained stable and the incidence of HCV-related HCC showed a major increase. During the coming years, we expect to improve our ability to prevent and effectively treat viral hepatitis A-E, resulting in the control of these global infections and the elimination of their associated morbidities and mortalities.
Cognitive radio testbed for Digital Beamforming of satellite communication

Digital Beamforming (DB) in satellite communication (SATCOM) has drawn significant attention in recent years. DB design is flexible and adaptive among frequencies, bandwidths, and interferences. In this work, we design a cognitive radio testbed for SATCOM for digital beamforming design and implementation. The testbed is capable of simultaneously capturing signals from multiple antennas. Considering the conditions of jamming or interference, the design implements spectrum detection and compressive sensing for channel condition monitoring in a real time. Using the analyzed jammer and interference information, the incoming signal can be moved into a different frequency where the channel is vacant or at least meets acceptable conditions. The beamforming design is also adaptive to the frequency where each beam is weighted differently for a given channel condition. In addition, the satellite antenna array is used to determine the signal direction of arrival (DoA), The DB is capable of forming the beam in the direction that avoids interference and jamming. Moreover, the detection of the jamming signal direction can help localize the jammer. In the testbed design, a Universal Software Radio Peripheral (USRP) is used as a radio frequency (RF) front end component and GNU radio connecting to computer as signal processing back end. The system architecture includes the transponder receiver. And a USRP ×310 with twinRx receiver is capable of obtaining multiple copies of the signal captured by multiple receiving antennas.
Hardware-in-the-loop simulation of DC microgrid with Multi-Agent System for emergency demand response

This paper presents the real-time hardware-in-the-loop simulation (HILS) of DC microgrids containing multiple distributed resources (DRs) such as a battery energy storage system, a small distributed generator and a smart DC load. The power grid and the DRs are developed in the real-time simulation software, specifically Opal-RT RT-LAB software. The controllers of the DRs are developed as hardware devices using AVR microcontroller named as ATMega-128. The simulation model and hardware devices are integrated in the HILS framework. Each controller of the DRs acts as an intelligent agent that can communicate and cooperate with the coordinator and other agents. Emergency demand response problems are applied to the HILS setup for the performance verification.
The business case for SDGs: an analysis of inclusive business models in emerging economies

ABSTRACT In September 2015, the Sustainable Development Goals (SDGs) were endorsed by the United Nations and adopted by all 193 Member States. The SDGs integrate the 5P’s: People, Planet, Prosperity, Peace, and Partnership and clearly stress the need for all stakeholders to collaborate to create a sustainable world. Most importantly, the SDGs appeal to the central and diverse role that the business sector can play to deliver on the SDGs. This paper provides an analysis of inclusive business (IB) models as market-based solutions to contribute to the achievement of the SDGs and benefit those at the Base of the Pyramid (BoP). We investigate the IB models and their social impact in 20 organizations from emerging economies across five different sectors. The findings should help increase the uptake and scale of quality IB models and practices among the private sector, development communities, and governments to promote inclusive economic growth and social impact.
Quantitative study of salivary secretion in Parkinson's disease

We examined basal and reflex salivary flow rate and composition in 46 patients with Parkinson's disease (PD), both in off and on conditions, compared to 13 age‐matched controls without underlying disease or treatment affecting autonomic function. Whole saliva was collected 12 hours after withdrawal of dopaminergic drugs and at the peak of levodopa‐induced motor improvement. Twenty‐three of the 46 PD patients had received domperidone a week before the study. Basal salivary flow rate was significantly lower in PD patients in the off state compared to controls (P < 0.005). Levodopa increased salivary flow rate (P < 0.05) both in the domperidone‐pretreated and untreated groups. Citric acid stimulated salivary flow rate in both the off and on states in PD patients. This effect was higher in the domperidone‐pretreated patients. Salivary concentration of sodium, chloride, and amylase was higher in PD patients than in controls and was not affected by levodopa or domperidone treatment. Levodopa stimulates both basal and reflex salivary flow rate in PD. The mechanism appears to be central, as the effect is not blocked by domperidone. Domperidone may have a peripheral effect that potentiates reflex salivary secretion. Salivary composition is abnormal in PD and is not affected by levodopa treatment. © 2006 Movement Disorder Society
The Conserved Phenylalanine in the Transmembrane Domain Enhances Heteromeric Interactions of Syndecans*

The transmembrane domain (TMD) of the syndecans, a family of transmembrane heparin sulfate proteoglycans, is involved in forming homo- and heterodimers and oligomers that transmit signaling events. Recently, we reported that the unique phenylalanine in TMD positively regulates intramolecular interactions of syndecan-2. Besides the unique phenylalanine, syndecan-2 contains a conserved phenylalanine (SDC2-Phe-169) that is present in all syndecan TMDs, but its function has not been determined. We therefore investigated the structural role of SDC2-Phe-169 in syndecan TMDs. Replacement of SDC2-Phe-169 by tyrosine (S2F169Y) did not affect SDS-resistant homodimer formation but significantly reduced SDS-resistant heterodimer formation between syndecan-2 and -4, suggesting that SDC2-Phe-169 is involved in the heterodimerization/oligomerization of syndecans. Similarly, in an in vitro binding assay, a syndecan-2 mutant (S2(F169Y)) showed a significantly reduced interaction with syndecan-4. FRET assays showed that heteromolecular interactions between syndecan-2 and -4 were reduced in HEK293T cells transfected with S2(F169Y) compared with syndecan-2. Moreover, S2(F169Y) reduced downstream reactions mediated by the heterodimerization of syndecan-2 and -4, including Rac activity, cell migration, membrane localization of PKCα, and focal adhesion formation. The conserved phenylalanine in syndecan-1 and -3 also showed heterodimeric interaction with syndecan-2 and -4. Taken together, these findings suggest that the conserved phenylalanine in the TMD of syndecans is crucial in regulating heteromeric interactions of syndecans.
The potential impacts of climate change on the Malaysian rice economy

The economic impacts of climate change on rice production in peninsular Malaysia were evaluated by using a simulation analysis. The crop model ORYZA 2000 was used to simulate rice growth and production. Variety MR 219 was used in the simulation of rice production from eight granary areas of peninsular Malaysia from 1999–2007. With increase in temperature of 2°C and at the current CO5 level, the model predicted decline in yield. With increase of CO5 concentration from 383 to 574ppm and with 2°C rise in temperature, the model predicted decline in rice production and also negative effect on rice economy. The findings indicate that the reduction in yield under the scenario of increase in temperature of 2°C was 0.36 metric tonne per hectare and the economic loss of RM162, 530.53 per year. Under the scenario of both increases in temperature and CO2 level, the reduction in yield was 0.69 metric tonne per hectare. This can be translated to the economic loss of RM299,145.10 per year for the peninsular Malaysia. Some adaptation and mitigation strategies to overcome the adverse effects of climate change on rice production are recommended.
Avian trichomoniasis: a study of lesions and relative prevalence in a variety of captive and free-living bird species as seen in an Australian avian practice.

BACKGROUND Studies of avian trichomoniasis in the literature are limited to some extent, often being confined to a single bird species or group of species within a bird Order. Some incidence studies have been reported for free-living birds, and occasionally for captive birds. Very few reports describe the prevalence and types of lesions seen for a wide range of bird species, especially from a clinical perspective. METHODS Retrospective study of avian practice records from a 10-year period. Emphasis on the types of presentations and relative prevalence of trichomoniasis in a variety of captive and free-living bird species encountered in Australian avian practice. RESULTS The occurrence of trichomoniasis in several novel species (lorikeets, corvids and a cuckoo species), plus its distinctive presentation in southern boobook owls (Ninox boobook), is documented. CONCLUSION Trichomoniasis should be a differential diagnosis for birds presenting with regurgitation or upper gastrointestinal abscesses, even if motile trichomonads are not found in wet preparations from crop washes or lesions.