Miracle-dz/UniFAR-FTUs huggingface dataset:
Farm level survey of spore‐forming bacteria on four dairy farms in the Waikato region of New Zealand

The aim of our study was to determine the occurrence and diversity of economically important spore‐forming bacteria in New Zealand dairy farm systems. Farm dairy effluent (FDE) collected from Waikato dairy farms were tested for the presence of spore‐forming bacteria, using a new culture‐based methodology followed by genomic analysis. An enrichment step in which samples were inoculated in cooked meat glucose starch broth under anaerobic conditions, aided in the differential isolation of Bacillus and Clostridium species. Furthermore, the use of molecular methods such as ERIC genotyping, 16S rRNA gene sequence analysis identified different spore‐forming bacteria present in FDE. C. sporogenes signature PCR gave further information on the phylogenetic relationship of the different Clostridium spp. isolated in this study. In total 19 Bacillus spp. , 5 Paenibacillus spp. and 17 Clostridium spp. were isolated from farm dairy effluent. Sequence types similar to economically important food spoilage bacteria viz: C. butyricum, C. sporogenes and members of the Paenibacillus Genus were isolated from all four farms, whereas, sequence types similar to potential toxigenic, B. cereus, C. perfringens, C. butyricum, and C. botulinum were found on at least three of the farms. Sampling of farm dairy effluent provides a good indicator of farm level prevalence of bacterial load as it is used to irrigate dairy pasture in New Zealand. This study highlights the presence of various spore‐forming bacteria in dairy waste water and indicates the implementation of good hygienic farm practices and dairy waste effluent management.
Polymer-DNA Nanoparticle-Induced CXCR4 Overexpression Improves Stem Cell Engraftment and Tissue Regeneration in a Mouse Hindlimb Ischemia Model

Peripheral arterial disease affects nearly 202 million individuals worldwide, sometimes leading to non-healing ulcers or limb amputations in severe cases. Genetically modified stem cells offer potential advantages for therapeutically inducing angiogenesis via augmented paracrine release mechanisms and tuned dynamic responses to environmental stimuli at disease sites. Here, we report the application of nanoparticle-induced CXCR4-overexpressing stem cells in a mouse hindlimb ischemia model. We found that CXCR4 overexpression improved stem cell survival, modulated inflammation in situ, and accelerated blood reperfusion. These effects, unexpectedly, led to complete limb salvage and skeletal muscle repair, markedly outperforming the efficacy of the conventional angiogenic factor control, VEGF. Importantly, assessment of CXCR4-overexpressing stem cells in vitro revealed that CXCR4 overexpression induced changes in paracrine signaling of stem cells, promoting a therapeutically desirable pro-angiogenic and anti-inflammatory phenotype. These results suggest that nanoparticle-induced CXCR4 overexpression may promote favorable phenotypic changes and therapeutic efficacy of stem cells in response to the ischemic environment.
First Insight into the Genome Sequence of Clostridium vincentii DSM 10228, Isolated from Sediment of the McMurdo Ice Shelf, Antarctica

ABSTRACT Clostridium vincentii is an obligate anaerobic, saccharophilic, psychrophilic, Gram-positive, motile, and rod-shaped bacterium. It was isolated from a pond sediment of the McMurdo Ice Shelf, Antarctica. C. vincentii produces acetate and formate as main fermentation products. The draft genome consists of one chromosome (3.506 Mb) with 3,379 predicted protein-encoding genes.
Protocoled resuscitation and the prevention of acute kidney injury

Purpose of reviewAcute kidney injury (AKI) occurrence in critically ill patients is common and is associated with a substantial increase in morbidity and mortality. The scope of this review is to summarize the most recent evidence-based knowledge for prevention of AKI. Recent findingsRecent recommendations for prevention of AKI in ICU patients are all ‘negative’ and, similarly, the most recent and updated guidelines about major topic areas of interest for AKI, including definition and classification, prevention, and pharmacologic treatment, have failed to identify single evidence-based recommendations for prevention and treatment of AKI. Therefore, the evaluation and management of AKI should be guided by clinical algorithms aiming to protocolized hemodynamic optimization, metabolic control, monitoring of intra-abdominal hypertension, use of diuretics to control fluid overload, and careful management of nephrotoxic factors. SummaryKey components of optimal AKI prevention include maintenance of renal perfusion and avoidance of precipitating factors. Adequate renal blood flow maintenance is the first strategy to employ not only to assure renal oxygenation, but also to prevent nephrotoxic drugs-associated AKI. Many potential therapies and interventions are on the horizon, but most of the future research will need to focus more on a step-wise, protocoled, kidney-oriented approach, than on single treatments.
Event-based neural computing on an autonomous mobile platform

Living organisms are capable of autonomously adapting to dynamically changing environments by receiving inputs from highly specialized sensory organs and elaborating them on the same parallel, power-efficient neural substrate. In this paper we present a prototype for a comprehensive integrated platform that allows replicating principles of neural information processing in real-time. Our system consists of (a) an autonomous mobile robotic platform, (b) on-board actuators and multiple (neuromorphic) sensors, and (c) the SpiNNaker computing system, a configurable neural architecture for exploration of parallel, brain-inspired models. The simulation of neurally inspired perception and reasoning algorithms is performed in real-time by distributed, low-power, low-latency event-driven computing nodes, which can be flexibly configured using C or specialized neural languages such as PyNN and Nengo. We conclude by demonstrating the platform in two experimental scenarios, exhibiting real-world closed loop behavior consisting of environmental perception, reasoning and execution of adequate motor actions.
Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe

A central step in the initiation of chromosomal DNA replication in eukaryotes is the assembly of pre-replicative complex (pre-RC) at late M and early G1 phase of the cell cycles. Since 1973, four proteins or protein complexes, including cell division control protein 6 (Cdc6)/Cdc18, minichromosome maintenance protein complex, origin recognition complex (ORC), and Cdt1, are known components of the pre-RC. Previously, we reported that a non-ORC protein binds to the essential element Δ9 of the Schizosaccharomyces pombe DNA-replication origin ARS3001. In this study, we identified that the non-ORC protein is Sap1. Like ORC, Sap1 binds to DNA origins during cell growth cycles. But unlike ORC, which binds to asymmetric AT-rich sequences through its nine AT-hook motifs, Sap1 preferentially binds to a DNA sequence of 5′-(A/T)n(C/G)(A/T)9–10(G/C)(A/T)n-3′ (n ≥ 1). We also found that Sap1 and ORC physically interact. We further demonstrated that Sap1 is required for the assembly of the pre-RC because of its essential role in recruiting Cdc18 to DNA origins. Thus, we conclude that Sap1 is a replication-initiation factor that directly participates in the assembly of the pre-RC. DNA-replication origins in fission yeast are defined by possessing two essential elements with one bound by ORC and the other by Sap1.
How to use linguistic instruments for object-oriented analysis

One of object orientation's main limitations is the object-oriented analysis process's immaturity. This article proposes an approach that is based on using linguistic information from information specifications to apply during this process. Our method helps to analyze this information semantically and syntactically and employs a semi-formal procedure to extract an object-oriented system's components.
Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis

Significance Genome-scale models of metabolism are important tools for metabolic engineering and production strain development. We present an experimentally validated and manually curated model of metabolism in Synechococcus elongatus PCC 7942 that (i) leads to discovery of unique metabolic characteristics, such as the importance of a truncated, linear TCA pathway, (ii) highlights poorly understood areas of metabolism as exemplified by knowledge gaps in nucleotide salvage, and (iii) accurately quantifies light input and self-shading. We now have a metabolic model that can be used as a basis for metabolic design in S. elongatus. The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable obligate phototroph that is being developed for the bioproduction of high-value chemicals. Genome-scale models (GEMs) have been successfully used to assess and engineer cellular metabolism; however, GEMs of phototrophic metabolism have been limited by the lack of experimental datasets for model validation and the challenges of incorporating photon uptake. Here, we develop a GEM of metabolism in S. elongatus using random barcode transposon site sequencing (RB-TnSeq) essential gene and physiological data specific to photoautotrophic metabolism. The model explicitly describes photon absorption and accounts for shading, resulting in the characteristic linear growth curve of photoautotrophs. GEM predictions of gene essentiality were compared with data obtained from recent dense-transposon mutagenesis experiments. This dataset allowed major improvements to the accuracy of the model. Furthermore, discrepancies between GEM predictions and the in vivo dataset revealed biological characteristics, such as the importance of a truncated, linear TCA pathway, low flux toward amino acid synthesis from photorespiration, and knowledge gaps within nucleotide metabolism. Coupling of strong experimental support and photoautotrophic modeling methods thus resulted in a highly accurate model of S. elongatus metabolism that highlights previously unknown areas of S. elongatus biology.
Next-Generation Sequencing Confirms Presumed Nosocomial Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in the Netherlands

ABSTRACT Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) was detected in 2003 and rapidly became the predominant MRSA clade in the Netherlands. Studies have shown that transmissions are difficult to identify, since this MRSA variant represents a genetically homogenous clade when current typing techniques are used. Here, next-generation sequencing was performed on 206 LA-MRSA isolates to assess the capability of LA-MRSA to be transmitted between humans. The usefulness of single nucleotide variants (SNVs), the composition of the SCCmec region, and the presence of plasmids to identify transmission of LA-MRSA were assessed. In total, 30 presumed putative nosocomial transmission events and 2 LA-MRSA outbreaks were studied; in most cases, SNV analysis revealed that the isolates of the index patient and the contact(s) clustered closely together. In three presumed events, the isolates did not cluster together, indicating that transmission was unlikely. The composition of the SCCmec region corroborated these findings. However, plasmid identification did not support our SNV analysis, since different plasmids were present in several cases where SNV and SCCmec analysis suggested that transmission was likely. Next-generation sequencing shows that transmission of LA-MRSA does occur in Dutch health care settings. Transmission was identified based on SNV analysis combined with epidemiological data and in the context of epidemiologically related and unrelated isolates. Analysis of the SCCmec region provided limited, albeit useful, information to corroborate conclusions on transmissions, but plasmid identification did not. IMPORTANCE In 2003, a variant of methicillin-resistant Staphylococcus aureus (MRSA) isolated from pigs was also found in pig farmers in France and the Netherlands. Soon thereafter, this livestock-associated MRSA (LA-MRSA) was identified in many other countries. Transmission of LA-MRSA between humans, particularly in the health care setting, is regarded to occur sporadically. Moreover, studies that describe LA-MRSA transmission used molecular characterization of isolates with limited discriminatory power, making the validity of the conclusion that transmission occurred questionable. In our study, we sequenced the complete genomes of 206 LA-MRSA isolates, obtained from more than 30 presumed LA-MRSA transmission events. Analysis of the data showed that transmission of LA-MRSA between humans had indeed occurred in more than 90% of these events. We conclude that transmission of LA-MRSA between humans does occur in Dutch health care settings; therefore, a decision to discontinue the search and destroy policy for LA-MRSA should be taken with caution.
Rossby Waves in the Tropical North Pacific and Their Role in Decadal Thermocline Variability

Abstract A band of enhanced thermocline variability at 10°–15°N in the Pacific found in nature also occurs in an ocean general circulation model forced with observed fluxes of momentum, heat, and freshwater over the period 1958–97. The variability in the model is primarily associated with long baroclinic Rossby waves characterized by periods in the decadal range (7–10 yr). The waves are forced by westward propagating Ekman pumping anomalies east of the date line and propagate at a speed of ∼13 cm s−1, which is slower than the phase speed of the first mode unforced baroclinic waves (15–16 cm s−1). West of the date line, the correlations between thermocline displacements and local Ekman pumping are relatively small, and the ocean signals have a phase speed of ∼20 cm s−1, very similar to the phase speed of the first baroclinic mode in the western half of the basin (18–20 cm s−1). The phase speeds of the ocean model signals have been estimated using cospectral analysis, while the WKB approximation has been us.
ANTIFERTILITY ACTIVITY OF MOMORDICA CHARANTIA DESCOURT PULP AND SEED HYDROALCOHOLIC EXTRACT

Momordica charantia Descourt (Cucurbetaceae) known as Karela is an extremely bitter vegetable, commonly found in India. M. charantia had reported anticancer, antidiabetic, antihypertensive, anti- inflammation and antioxidant properties. It is used as antifertility agent in folklore; however no studies have been done on its antifertility action. Anti-fertility potential of the M. charantia hydroalcoholic extracts of seed and pulp was explored on in vitro spermicidal, antiovulatory, in vivo estrogenic and anti-estrogenic activity along with uterus histopathology. Data were presented as M ± SEM and analyzed with ANOVA followed by ttest. MCHS and MCHP are tested for its antifertility activity at doses of 200 mg/kg and 400 mg/kg, orally as it was found safe on acute dosing of 2000 mg/kg. Pulp extract at 1280 μg/ml concentration caused significant damage to the sperm membrane integrity as evidenced by the reduction in sperm viability and tail curling. Administration of pulp extract at 400 mg/kg dose caused significant (p < 0.001) increases in uterine weight in immature rats while co-administration with ethinylestradiol decreased the uterus weight and increased the height of luminal epithelium with stimulated glands. Pulp extract at 400 mg/kg dose also caused significant (p < 0.001) prolongation estrous cycle and diestrous phase. Among the two extracts tested at two different doses, the hydroalcoholic pulp extract of M. charantia at 400 mg/kg was found to exhibit antifertility activity may be due to rich presence of triterpenoidal glycosides, flavonoids and alkaloids.
Identification of the Three Genes Involved in Controlling Production of a Phytotoxin Tropolone in Burkholderia plantarii

ABSTRACT Tropolone, a phytotoxin produced by Burkholderia plantarii, causes rice seedling blight. To identify genes involved in tropolone synthesis, we systematically constructed mutations in the genes encoding 55 histidine kinases and 72 response regulators. From the resulting defective strains, we isolated three mutants, KE1, KE2, and KE3, in which tropolone production was repressed. The deleted genes of these mutants were named troR1, troK, and troR2, respectively. The mutant strains did not cause rice seedling blight, and complementation experiments indicated that TroR1, TroK, and TroR2 were involved in the synthesis of tropolone in B. plantarii. However, tropolone synthesis was repressed in the TroR1 D52A, TroK H253A, and TroR2 D46A site-directed mutants. These results suggest that the putative sensor kinase (TroK) and two response regulators (TroR1 and TroR2) control the production of tropolone in B. plantarii. IMPORTANCE A two-component system is normally composed of a sensor histidine kinase (HK) and a cognate response regulator (RR) pair. In this study, HK (TroK) and two RRs (TroR1 and TroR2) were found to be involved in controlling tropolone production in B. plantarii. These three genes may be part of a bacterial signal transduction network. Such networks are thought to exist in other bacteria to regulate phytotoxin production, as well as environmental adaptation and signal transduction.
Fast Aberration Measurement in Multi-Dimensional STEM

The main resolution limits in high-performance (S)TEM are due to the imperfections or ‘aberrations’ of the electron lenses. Correction of these aberrations requires the ability to quickly and accurately measure lens aberrations to align or ‘tune’ an aberration-corrector. The conventional method to measure aberrations in the TEM is to record a series of bright field (BF) images in a Zemlin tableau. However, the reciprocity-equivalent method in STEM of recording a series of tilted BF images is inherently inefficient if only a single BF detector is available. Aberration measurement methods based on recording and analyzing the whole scattering distribution (Ronchigram) provide an efficient use of the signal available in the STEM, however, normally only a small number of probe positions is used [3, 4]. We have recently demonstrated a method based on acquiring Ronchigrams at a multiplicity of probe positions [5]. This procedure results in 4-dimensional dataset, which can be transformed to give an array of real-space images of a sample. Cross-correlating the resulting images gives the gradient of the aberration function, from which the aberrations are determined by a least-squares fit [5]. This procedure provides rapid, accurate aberration measurements and can in principle be extended to arbitrary-order measurements. Figure 1 shows an example aberration measurement based on this method. A series of Ronchigrams was recorded with a nominal 1 nm step between probe positions. A typical Ronchigram is shown, along with measured and fitted shifts, which are used to find the aberration function.
Surface Modification of Electromagnetic Railgun Components

Copper and aluminum used for rail and armature materials in electromagnetic railgun systems undergo severe degradation during the EM gun operation. The extent of this degradation is especially severe in guns operated at high energy levels or designed for repeated firings. In an effort to improve surface properties of the copper rail, armature, and sabot materials, the technique of metal ion implantation using a vacuum arc ion source has been employed. Preliminary tests have been conducted to identify the best implant species to improve spark erosion resistance, scratch resistance and hardness. The implanted species included Al, Ti, Cr, Ni, Ta, Ag, and W. The implantation energy range and dose varied between 100–180 KeV and 0.4 to 2 × 10 17 cm -2 , respectively . Several analytical techniques were also used to assess the effect of implanted species. These included Rutherford Back Scattering (RBS), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Microhardness Measurements, Spark Erosion and Scratch Testing. It has been tentatively concluded that Ta and Ni implantation of the copper rail substantially improve wear and inhibit arc erosion. There is also sufficient evidence to indicate that implantation of the aluminum armature with Cr and Ta, involving two stages of implantation, will also improve its mechanical and wear properties.
Resonance frequencies of honeybee (Apis mellifera) wings

ABSTRACT During flight, insect wings bend and twist under the influence of aerodynamic and inertial forces. We tested whether wing resonance of honeybees (Apis mellifera) matches the wingbeat frequency, against the ‘stiff element’ hypothesis that the wing's first longitudinal mode exceeds the wingbeat frequency. Six bees were immobilized with their right wing pair outspread, and stimulated with a shaker while the normal modes were recorded with a scanning Doppler laser vibrometer. The lowest normal mode of the wings was the first longitudinal bending mode and, at 602±145 Hz, was greater than the wingbeat frequency of 234±13.9 Hz. Higher-order normal modes of the wing tended to incorporate nodal lines in the chordwise direction of the trailing edge, suggesting that their mode shape did not strongly resemble wing deformation during flapping flight. These results support the stiff element hypothesis for Apis mellifera. Summary: Normal modes of honeybee wings do not match the wingbeat frequency or harmonics, suggesting that the wings act as stiff elements when flapped.
Effect of Ginger Extract on Deltamethrin Induced Histomorphological and Immunohistochemical Changes in Testes of Albino Rats

The current study investigated the effect of ginger{Zingiberofficinale Roscoe(Zofficinale R.}extract on deltamethrin induced testicular damage in albino rats. Treating animals with deltamethrin at a dose level of 1/10 LD50, 3 days weekly for 6 weeks caused a decrease in body and testes weights. Remarkable decreases were also noted in sperm cell concentrations and sperm motility. In addition histopathological results revealed degeneration of spermatogenic cells, congestion of blood vessels and destruction of Leydige cells.The diameters of the seminiferous tubules and heights of their germinal epithelium were significantly reduced. Immunohistochemical results showed that Bax expression was increased in Leydige cells and p53 expression increased in spermatocytes of testes of deltamethrin treated rats. According to these results, deltamethrin induced oxidative stress and caused apoptosis in testes of albino rats. Treating animals with deltamethrin and ginger revealed an improvement in the histological changes observed in animals treated with deltamethrin and increased sperm concentration and motility. Moreover, ginger treatment leads to a decrease in the expression of p53 and bax. This effect of ginger extract may be attributed to its antioxidant activity. [Saber A. Sakrand Wael M. Al-Amoudi. Effect of Ginger Extract on Deltamethrin Induced Histomorphological and Immunohistochemical Changes in Testes of Albino Rats. Life Science Journal 2012; 9(1):771-778]. (ISSN: 1097-8135). http://www.lifesciencesite. com.111