Miracle-dz/UniFAR-FTUs huggingface dataset:
Community shifts and carbon translocation within metabolically-active rhizosphere microorganisms in grasslands under elevated CO 2

Abstract. The aim of this study was to identify the microbial communities that are actively involved in the assimilation of rhizosphere-C and are most sensitive in their activity to elevated atmospheric CO2 in a temperate semi-natural low-input grassland ecosystem. For this, we analyzed 13C signatures in microbial biomarker phospholipid fatty acids (PLFA) from an in-situ 13CO2 pulse-labeling experiment in the Giessen Free Air Carbon dioxide Enrichment grasslands (GiFACE, Germany) exposed to ambient and elevated (i.e. 50% above ambient) CO2 concentrations. Short-term 13C PLFA measurements at 3 h and 10 h after the pulse-labeling revealed very little to no 13C enrichment after 3 h in biomarker PLFAs and a much greater incorporation of new plant-C into fungal compared to bacterial PLFAs after 10 h. After a period of 11 months following the pulse-labeling experiment, the 13C enrichment of fungal PLFAs was still largely present but had decreased, while bacterial PLFAs were much more enriched in 13C compared to a few hours after the pulse-labeling. These results imply that new rhizodeposit-C is rapidly processed by fungal communities and only much later by the bacterial communities, which we attributed to either a fungal-mediated translocation of rhizosphere-C from the fungal to bacterial biomass or a preferential bacterial use of dead root or fungal necromass materials as C source over the direct utilization of fresh root-exudate C in these N-limited grassland ecosystems. Elevated CO2 caused an increase in the proportional 13C enrichment (relative to the universal biomarker 16:0) of the arbuscular mycorrhizal fungal biomarker PLFA 16:1ω5 and one gram-positive bacterial biomarker PLFA i16:0, but a decrease in the proportional 13C enrichment of 18:1ω9c, a commonly used though questionable fungal biomarker PLFA. This suggests enhanced fungal rhizodeposit-C assimilation only by arbuscular mycorrhizal fungal species under elevated CO2.
Supply constraints and house price dynamics: panel data evidence from England

We explore the impact of regulatory and physical supply constraints on house price levels and volatility in England. We hypothesize that house prices react more strongly to changes in income in more constrained locations and test this proposition using a unique panel dataset of 353 local authorities, ranging from 1974 to 2008. We use a policy reform and historical density as instruments to identify the endogenous constraints-measures and document that both regulatory and physical constraints have a strong positive causal effect on the long-run impact of income on house prices. Our counterfactual analysis suggests that average house prices in England in 2008 would be 21.4 percent lower if the planning system were completely relaxed. The standard deviation of prices during the sample period would be 29.7 percent lower. House prices (volatility) would be 9.9 (13.1) percent lower absent of scarcity constraints and 2.8 (3.6) percent lower if England were totally flat. JEL classification: G12, R11, R21, R31, R52.
Multifocal epithelial tumors and field cancerization: stroma as a primary determinant.

It is increasingly evident that cancer results from altered organ homeostasis rather than from deregulated control of single cells or groups of cells. This applies especially to epithelial cancer, the most common form of human solid tumors and a major cause of cancer lethality. In the vast majority of cases, in situ epithelial cancer lesions do not progress into malignancy, even if they harbor many of the genetic changes found in invasive and metastatic tumors. While changes in tumor stroma are frequently viewed as secondary to changes in the epithelium, recent evidence indicates that they can play a primary role in both cancer progression and initiation. These processes may explain the phenomenon of field cancerization, i.e., the occurrence of multifocal and recurrent epithelial tumors that are preceded by and associated with widespread changes of surrounding tissue or organ "fields. "
Detecting higher-level similarity patterns in programs

Cloning in software systems is known to create problems during software maintenance. Several techniques have been proposed to detect the same or similar code fragments in software, so-called simple clones. While the knowledge of simple clones is useful, detecting design-level similarities in software could ease maintenance even further, and also help us identify reuse opportunities. We observed that recurring patterns of simple clones - so-called structural clones - often indicate the presence of interesting design-level similarities. An example would be patterns of collaborating classes or components. Finding structural clones that signify potentially useful design information requires efficient techniques to analyze the bulk of simple clone data and making non-trivial inferences based on the abstracted information. In this paper, we describe a practical solution to the problem of detecting some basic, but useful, types of design-level similarities such as groups of highly similar classes or files. First, we detect simple clones by applying conventional token-based techniques. Then we find the patterns of co-occurring clones in different files using the Frequent Itemset Mining (FIM) technique. Finally, we perform file clustering to detect those clusters of highly similar files that are likely to contribute to a design-level similarity pattern. The novelty of our approach is application of data mining techniques to detect design level similarities. Experiments confirmed that our method finds many useful structural clones and scales up to big programs. The paper describes our method for structural clone detection, a prototype tool called Clone Miner that implements the method and experimental results.
International Journal of Nanomedicine Dovepress Bactericidal Effects of Silver plus Titanium Dioxide-coated Endotracheal Tubes on Pseudomonas Aeruginosa and Staphylococcus Aureus

Purpose: Ventilator-associated pneumonia (VAP) is a nosocomial infection resulting in significant morbidity and mortality. Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus) are pathogens associated with VAP. Silver (Ag) coating of endotracheal tubes (ETTs) reduces bacterial colonization, however titanium dioxide (TiO 2) coating has not been studied. Methods: Five types of ETT coatings were applied over silica layer: Ag, solgel TiO 2 , solgel TiO 2 with Ag, Degussa P25 TiO 2 (Degussa TiO 2), and Degussa TiO 2 with Ag. After ETTs were incubated with P. aeruginosa or S. aureus; colonization was determined quantitatively. Results: Pseudomonas aeruginosa and S. aureus grew for 5 days on standard ETTs. Compared to standard ETTs, P. aeruginosa growth was significantly inhibited by solgel TiO 2 with Ag at 24 hours, and by Degussa TiO 2 with Ag at 24 and 48 hours after inoculation. No significant difference in S. aureus growth was observed between the control and any of the five coatings for 5 days. Conclusion: In vitro, solgel TiO 2 with Ag and Degussa TiO 2 with Ag both attenuated P. aeruginosa growth, but demonstrated no effect on S. aureus colonization. Further studies using alternative coating and incorporating UV light exposure are needed to identify their potential utility in reducing VAP.
RESISTANCE OF CONCRETE TO FREEZING AND THAWING

This study, aimed at improving the freeze-thaw resistance of concrete, consists of three parts. Part I evaluates parameters affecting the freeze-thaw durability of concrete. A modification of the existing standard of method for determining the durability factor of concrete specimens is proposed, and a new procedure for fundamental transverse frequency (used in durability factor calculations) has been developed. Part II focuses on developing better methods for identifying nondurable aggregates, and has resulted in a rapid new test based on the hydraulic fracture of aggregates. Part III describes field experiments to evaluate the freeze-thaw resistance of a number of specified concrete mixes and the use of sealants to mitigate D-cracking. Preliminary field performance results are presented.
(Post-) Genomic approaches to tackle drug resistance in Leishmania

SUMMARY Leishmaniasis, like other neglected diseases is characterized by a small arsenal of drugs for its control. To safeguard the efficacy of current drugs and guide the development of new ones it is thus of utmost importance to acquire a deep understanding of the phenomenon of drug resistance and its link with treatment outcome. We discuss here how (post-)genomic approaches may contribute to this purpose. We highlight the need for a clear definition of the phenotypes under consideration: innate and acquired resistance versus treatment failure. We provide a recent update of our knowledge on the Leishmania genome structure and dynamics, and compare the contribution of targeted and untargeted methods for the understanding of drug resistance and show their limits. We also present the main assays allowing the experimental validation of the genes putatively involved in drug resistance. The importance of analysing information downstream of the genome is stressed and further illustrated by recent metabolomics findings. Finally, the attention is called onto the challenges for implementing the acquired knowledge to the benefit of the patients and the population at risk.
Resting and maximal forearm skin blood flows are reduced in hypertension.

To find whether the vasodilator capacity of nonacral skin is reduced in hypertension, we measured forearm blood flow by venous occlusion plethysmography in 10 seated normotensive (mean +/- SD mean arterial pressure, 94 +/- 5 mm Hg) and 10 hypertensive (112 +/- 9 mm Hg) men at rest for 39 minutes while the forearm was heated with water at 42 degrees C, a maneuver known to selectively and maximally vasodilate skin. Blood pressure, measured every 5 minutes, did not change with heating. We found that in the normotensive group resting forearm blood flow was higher (3.64 +/- 1.12 versus 2.48 +/- 0.58 ml/100 ml tissue per minute, p less than 0.001; normotensive group versus hypertensive group) and resting forearm vascular resistance lower (30.17 +/- 10.99 versus 48.88 +/- 17.37 mm Hg.min.100 ml tissue per minute, p less than 0.05; normotensive group versus hypertensive group), and maximal forearm blood flow with local heating was higher (29.32 +/- 11.99 versus 18.19 +/- 4.50 ml/100 tissue per minute, p less than 0.018; normotensive group versus hypertensive group and vascular resistance lower (4.07 +/- 1.04 versus 6.54 +/- 1.17 mm Hg.min.100 ml tissue per minute, p less than 0.005; normotensive group versus hypertensive group). To find whether this degree and duration of local warming maximally vasodilated the skin in hypertensive subjects (as it does in normotensive subjects), we measured forearm skin blood flow before and during local heating plus 10 minutes of ischemia using a laser Doppler flowmeter. (ABSTRACT TRUNCATED AT 250 WORDS)
Formaldehyde exposure and leukemia: Critical review and reevaluation of the results from a study that is the focus for evidence of biological plausibility

Abstract A recent study (Zhang et al., 2010) has provided results attributed to aneuploidy in circulating stem cells that has been characterized as providing potential support for proposed mechanisms for formaldehyde to impact bone marrow. A critical review of the study, as well as a reanalysis of the underlying data, was performed and the results of this reanalysis suggested factors other than formaldehyde exposure may have contributed to the effects reported. In addition, although the authors stated in their paper that “all scorable metaphase spreads on each slide were analyzed, and a minimum of 150 cells per subject was scored,” this protocol was not followed. In fact, the protocol to evaluate the presence of monosomy 7 or trisomy 8 was followed for three or less samples in exposed workers and six or less samples in non-exposed workers. In addition, the assays used (CFU-GM) do not actually measure the proposed events in primitive cells involved in the development of acute myeloid leukemia. Evaluation of these data indicates that the aneuploidy measured could not have arisen in vivo, but rather arose during in vitro culture. The results of our critical review and reanalysis of the data, in combination with recent toxicological and mechanistic studies, do not support a mechanism for a causal association between formaldehyde exposure and myeloid or lymphoid malignancies.
Large scale structure and supersymmetric inflation without fine tuning.

We explore constraints on the spectral index $n$ of density fluctuations and the neutrino energy density fraction $\Omega_{HDM}$, employing data from a variety of large scale observations. The best fits occur for $n\approx 1$ and $\Omega_{HDM} \approx 0.15 - 0.30$, over a range of Hubble constants $40-60$ km s$^{-1}$ Mpc$^{-1}$. We present a new class of inflationary models based on realistic supersymmetric grand unified theories which do not have the usual `fine tuning' problems. The amplitude of primordial density fluctuations, in particular, is found to be proportional to $(M_X /M_P)^2$, where $M_X (M_P)$ denote the GUT (Planck) scale, which is reminiscent of cosmic strings! The spectral index $n = 0.98$, in excellent agreement with the observations provided the dark matter is a mixture of `cold' and `hot' components.
Nutrient Flow Scenarios for Sustainable Smallholder Farming Systems in Southwestern Burkina Faso

The CGIAR Research Program on Dryland Systems aims to improve the lives of 1.6 billion people and mitigate land and resource degradation in 3 billion hectares covering the world’s dry areas. Dryland Systems engages in integrated agricultural systems research to address key socioeconomic and biophysical constraints that affect food security, equitable and sustainable land and natural resource management, and the livelihoods of poor and marginalized dryland communities. The program unifies eight CGIAR Centres and uses unique partnership platforms to bind together scientific research results with the skills and capacities of national agricultural research systems (NARS), advanced research institutes (ARIs), non-governmental and civil society organizations, the private sector
ANALISIS PENGARUH SERTIFIKAT BANK INDONESIA SYARIAH (SBIS), INFLASI DAN JAKARTA ISLAMIC INDEX (JII) TERHADAP NILAI AKTIVA BERSIH (NAB) DANAREKSA SYARIAH BERIMBANG (Skripsi)

Tujuan dari penelitian ini adalah untuk mengetahui pengaruh Sertifikat Bank Indonesia Syariah (SBIS), Inflasi, dan Jakarta Islamic Index (JII), terhadap Nilai Aktiva Berisih (NSB) Danareksa Syariah Berimbang periode Oktober 2010 sampai dengan Maret 2013. Penelitain ini menggunakan data sekunder kuantitatif, yaitu data bulanan dari Bank Indonesia (BI), Badan Pengawas Pasar Modal (BAPEPAM), dan Bursa Efek Indonesia (BEI). Analisis regresi linear berganda yang digunakan dalam penelitian ini yaitu program SPSS. Hasil estimasi persamaan NAB reksa dana syariah menunjukkan nilai koefisien determinasi R Square adalah sebesar 72.9%, maka hal ini dapat menjelaskan kontribusi SBIS, Inflasi, dan JII dalam mempengaruhi NAB Danareksa Syariah Berimbang sebesar 72.9% dan sisanya 27.1% dijelaskan oleh variabel di luar penelitian. Variabel JII merupakan variabel yang paling dominan dan berpengaruh secara signifikan sedangkan SBIS dan Inflasi tidak memiliki pengaruh terhhadap NAB Danareksa Syariah Berimbang
Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography

Rabbit hemorrhagic disease, first described in China in 1984, causes hemorrhagic necrosis of the liver. Its etiological agent, rabbit hemorrhagic disease virus (RHDV), belongs to the Lagovirus genus in the family Caliciviridae. The detailed molecular structure of any lagovirus capsid has yet to be determined. Here, we report a cryo-electron microscopic (cryoEM) reconstruction of wild-type RHDV at 6.5 Å resolution and the crystal structures of the shell (S) and protruding (P) domains of its major capsid protein, VP60, each at 2.0 Å resolution. From these data we built a complete atomic model of the RHDV capsid. VP60 has a conserved S domain and a specific P2 sub-domain that differs from those found in other caliciviruses. As seen in the shell portion of the RHDV cryoEM map, which was resolved to ∼5.5 Å, the N-terminal arm domain of VP60 folds back onto its cognate S domain. Sequence alignments of VP60 from six groups of RHDV isolates revealed seven regions of high variation that could be mapped onto the surface of the P2 sub-domain and suggested three putative pockets might be responsible for binding to histo-blood group antigens. A flexible loop in one of these regions was shown to interact with rabbit tissue cells and contains an important epitope for anti-RHDV antibody production. Our study provides a reliable, pseudo-atomic model of a Lagovirus and suggests a new candidate for an efficient vaccine that can be used to protect rabbits from RHDV infection.
Structural Abnormalities at Neuromuscular Synapses Lacking Multiple Syntrophin Isoforms

The syntrophins are modular adapter proteins that function by recruiting signaling molecules to the cytoskeleton via their direct association with proteins of the dystrophin protein family. We investigated the physiological function of β2-syntrophin by generating a line of mice lacking this syntrophin isoform. The β2-syntrophin null mice show no overt phenotype, or muscular dystrophy, and form structurally normal neuromuscular junctions (NMJs). To determine whether physiological consequences caused by the lack of β2-syntrophin were masked by compensation from the α-syntrophin isoform, we crossed these mice with our previously described α-syntrophin null mice to produce mice lacking both isoforms. The α/β2-syntrophin null mice have NMJs that are structurally more aberrant than those lacking only α-syntrophin. The NMJs of the α/β2-syntrophin null mice have fewer junctional folds than either parent strain, and the remaining folds are abnormally shaped with few openings to the synaptic space. The levels of acetylcholine receptors are reduced to 23% of wild type in mice lacking both syntrophin isoforms. Furthermore, the α/β2-syntrophin null mice ran significantly shorter distances on voluntary exercise wheels despite having normal neuromuscular junction transmission as determined by micro-electrode recording of endplate potentials. We conclude that both α-syntrophin and β2-syntrophin play distinct roles in forming and maintaining NMJ structure and that each syntrophin can partially compensate for the loss of the other.
Herpes Simplex Virus 2 Expresses a Novel Form of ICP34.5, a Major Viral Neurovirulence Factor, through Regulated Alternative Splicing

ABSTRACT Herpes simplex virus 1 (HSV-1) and HSV-2, two closely related neurotropic human herpesviruses, achieve neurotropism through ICP34.5, a major viral neurovirulence factor. In this report, in addition to the full-length 38-kDa protein (ICP34.5α), we identified a 28-kDa novel form of ICP34.5 (ICP34.5β) in HSV-2-infected cells. ICP34.5β is translated from unspliced ICP34.5 mRNA, with the retained intron introducing a premature stop codon. Thus, ICP34.5β lacks the C-terminal conserved GADD34 domain but includes 19 additional amino acids encoded by the intron. Although a fraction of both HSV-2 ICP34.5 proteins are detected in the nucleolus, ICP34.5α is predominantly located in cytoplasm, and ICP34.5β is mainly detected more diffusely in the nucleus. ICP34.5β is unable to counteract PKR-mediated eIF2 phosphorylation but does not interfere with ICP34.5α's function in this process. Efficient expression of ICP34.5β in cell culture assays is dependent on viral infection or expression of ICP27, a multifunctional immediate-early gene. The effect of ICP27 on the ICP34.5β protein level is attributed to its selective inhibition of ICP34.5 splicing, which results in increased expression of ICP34.5β but a reduced level of ICP34.5α. The C- terminal KH3 domain but not the RNA binding domain of ICP27 is required for its specific inhibition of ICP34.5 splicing and promotion of ICP34.5β expression. Our results suggest that the expression of ICP34.5α and ICP34.5β is tightly regulated in HSV-2 and likely contributes to viral pathogenesis.
STANDARDISATION OF PLANTING GEOMETRY IN AEROBIC RICE (Oryza sativa L.) UNDER DIFFERENT LEVELS OF DRIP FERTIGATION

Studies on Standardisation of planting geometry in aerobic rice (Oryza sativa L.) under different levels of drip fertigation was conducted during Kharif 2014 at ZARS, UAS, GKVK, Bengaluru. Experiment laid out in a factorial randomized complete block design with 13 treatments which were replicated thrice. The treatments constitutes 50 per cent of RDF (F1), 75 per cent of RDF (F2) and 100 per cent of RDF through Drip fertigation (F3) with four planting geometry 25 cm x 10 cm, 25 cm x 15 cm, 25 cm x 20 cm and 25 cm x 25 cm, with a control i.e., planting geometry of 25 cm x 25 cm with surface irrigation and soil application of RDF. The results revealed that, 100 per cent RDF through drip fertigation has recorded significantly higher productive tillers (601.73 m -2 ), grain (6115 kg ha -1 ) straw yield (8792 kg ha -1 ) and (kg ha-cm -1 ). Planting geometry of 25 cm x 15 cm recorded significantly higher productive tillers (516.61 m -2 ), grain (5954 kg ha -1 ) straw yield (8297 kg ha -1 ) and WUE (80.66 kg ha-cm -1 ). Interaction of planting geometry of 25 cm x 15 cm with 100 per cent RDF through drip fertigation has recorded significantly higher productive tillers (719.47 m -2 ), grain (6762 kg ha -1 ), straw yield (9186 kg ha -1 ) and WUE (91.59 kg ha-cm -1 ). Planting geometry of 25 cm x 15 cm with 100 per cent RDF through drip fertigation recorded higher gross, net returns and B: C ratio (` 121977, ` 75814 ha and 2.64, respectively).
Letter: treatment of autoimmune acute liver failure – beyond consensus guidelines

SIRS, We read with great interest and agreement the review article by Czaja 1 who reported the management of autoimmune hepatitis (AIH) beyond consensus guidelines. As he described in the review, ‘highly individualised clinical judgments are required at decision points that are outside confident guidelines, and these judgments can be difficult and controversial’. The aetiology of fulminant hepatitis in our unit was due to AIH in 29.3%, after the establishment of the international AIH criteria. In a recent Japanese nationwide survey, the number of patients with AIH showing the histological features of acute hepatitis, including acute liver failure (ALF), has been increasing. The US ALF Study Group reported that 58% of indeterminate ALF were considered autoimmune ALF. Therefore, AIH is a major aetiology of ALF worldwide. The survival rate without liver transplantation (LT) of patients with fulminant AIH is poor, 5 which is recognised everywhere around the world. LT should be considered, but in Japan where the serious problems of a shortage of donor livers exist, the treatment decision against immunosuppressive therapy is difficult. Czaja suggested that failure to improve within 2 weeks of immunosuppression indicates the need of emergency LT. We applaud his efforts for diagnosing and treating this intractable liver disease, and dare to present one uncertain but important data based on ‘low-quality clinical evidence and conflicting experiences’, as hepatologists struggling against intractable liver diseases, including AIH, in Japan. Mean duration between introduction of immunosuppression and onset of sepsis was 14.8 9.7 days in our autoimmune ALF patients (Figure 1). Therefore, we also suppose that the 2-week duration after introduction of immunosuppression is indeed a critical point for avoiding infectious complications and considering LT, although the most important treatment strategy is to diagnose and treat acute onset AIH before the development of ALF.