Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights into Denitrification in Methylotenera mobilis from Denitrification Pathway and Methanol Metabolism Mutants

ABSTRACT We investigated phenotypes of mutants of Methylotenera mobilis JLW8 with lesions in genes predicted to encode functions of the denitrification pathway, as well as mutants with mutations in methanol dehydrogenase-like structural genes xoxF1 and xoxF2, in order to obtain insights into denitrification and methanol metabolism by this bacterium. By monitoring the accumulation of nitrous oxide, we demonstrate that a periplasmic nitrate reductase, NAD(P)-linked and copper-containing nitrite reductases, and a nitric oxide reductase are involved in the denitrification pathway and that the pathway must be operational in aerobic conditions. However, only the assimilatory branch of the denitrification pathway was essential for growth on methanol in nitrate-supplemented medium. Mutants with mutations in each of the two xoxF genes maintained their ability to grow on methanol, but not the double XoxF mutant, suggesting that XoxF proteins act as methanol dehydrogenase enzymes in M. mobilis JLW8. Reduced levels of nitrous oxide accumulated by the XoxF mutants compared to the wild type suggest that these enzymes must be capable of donating electrons for denitrification.
Aalborg Universitet Optimal Power Scheduling for a Grid-Connected Hybrid PV-Wind-Battery Microgrid System

In this paper, a lineal mathematical model is proposed to schedule optimally the power references of the distributed energy resources in a grid-connected hybrid PVwind-battery microgrid. The optimization of the short term scheduling problem is addressed through a mixed-integer linear programming mathematical model, wherein the cost of energy purchased from the main grid is minimized and profits for selling energy generated by photovoltaic arrays are maximized by considering both physical constraints and requirements for a feasible deployment in the real system. The optimization model is tested by using a real-time simulation of the model and uploaded it in a digital control platform. The results show the economic benefit of the proposed optimal scheduling approach in two different scenarios.
Distinct ErbB2 receptor populations differentially interact with beta1 integrin in breast cancer cell models

ErbB2 is a member of the ErbB family of tyrosine kinase receptors that plays a major role in breast cancer progression. Located at the plasma membrane, ErbB2 forms large clusters in spite of the presence of growth factors. Beta1 integrin, membrane receptor of extracellular matrix proteins, regulates adhesion, migration and invasiveness of breast cancer cells. Physical interaction between beta1 integrin and ErbB2 has been suggested although published data are contradictory. The aim of the present work was to study the interaction between ErbB2 and beta1 integrin in different scenarios of expression and activation. We determined that beta1 integrin and ErbB2 colocalization is dependent on the expression level of both receptors exclusively in adherent cells. In suspension cells, lack of focal adhesions leave integrins free to diffuse on the plasma membrane and interact with ErbB2 even at low expression levels of both receptors. In adherent cells, high expression of beta1 integrin leaves unbound receptors outside focal complexes that diffuse within the plasma membrane and interact with ErbB2 membrane domains. Superresolution imaging showed the existence of two distinct populations of ErbB2: a major population located in large clusters and a minor population outside these structures. Upon ErbB2 overexpression, receptors outside large clusters can freely diffuse at the membrane and interact with integrins. These results reveal how expression levels of beta1 integrin and ErbB2 determine their frequency of colocalization and show that extracellular matrix proteins shape membrane clusters distribution, regulating ErbB2 and beta1 integrin activity in breast cancer cells.
Di-μ-chlorido-bis{chlorido[2-(2-furylmethyliminomethyl)pyridine-κ2 N,N′]nickel(II)}

The title dinuclear nickel(II) complex, [Ni2Cl4(C11H10N2O)2], lies on a centre of symmetry located at the centroid of the four-membered ring formed by the two Ni atoms and the bridging chloride ions. The NiII atom is five-coordinated in a square-pyramidal geometry by the imine and pyridine N atoms of the Schiff base ligand, and by one terminal and two bridging Cl atoms. The Ni⋯Ni distance is 3.506 (2) Å. The O atom of the furan substituent in the ligand unit is not involved in coordination to the Ni atom.
Transcriptomic and Metabolic Changes Associated with Photorespiratory Ammonium Accumulation in the Model Legume Lotus japonicus1[W]

Transcriptomic and metabolomic analysis of a plastidic glutamine synthetase mutant shows a coordinate repression of photorespiratory genes and accumulation of several key metabolites. The transcriptomic and metabolic consequences of the lack of plastidic glutamine (Gln) synthetase in the model legume Lotus japonicus were investigated. Wild-type and mutant plants lacking the plastidic isoform of Gln synthetase were grown in conditions that suppress photorespiration and then transferred for different lengths of time to photorespiratory conditions. Transcript and metabolite levels were determined at the different time points considered. Under photorespiratory active conditions, the mutant accumulated high levels of ammonium, followed by its subsequent decline. A coordinate repression of the photorespiratory genes was observed in the mutant background. This was part of a greater modulation of the transcriptome, especially in the mutant, that was paralleled by changes in the levels of several key metabolites. The data obtained for the mutant represent the first direct experimental evidence for a coordinate regulation of photorespiratory genes over time. Metabolomic analysis demonstrated that mutant plants under active photorespiratory conditions accumulated high levels of several amino acids and organic acids, including intermediates of the Krebs cycle. An increase in Gln levels was also detected in the mutant, which was paralleled by an increase in cytosolic Gln synthetase1 gene transcription and enzyme activity levels. The global panoramic of the transcripts and metabolites that changed in L. japonicus plants during the transfer from photorespiration-suppressed to photorespiration-active conditions highlighted the link between photorespiration and several other cellular processes, including central carbon metabolism, amino acid metabolism, and secondary metabolism.
Selection of electrogenic bacteria for microbial fuel cell in removing Victoria blue R from wastewater

ABSTRACT This study was conducted to select electrogenic bacteria from wastewater sludge. Phylogenetic analysis revealed that Proteobacteria was the dominant phylum in the microbial fuel cell (MFC) during the decomposition process of organic pollutants. Five culturable bacteria strains – namely, Bacillus subtilis, Flavobacterium sp. , Aeromonas hydrophila, Citrobacter freundii, and Stenotrophomonas sp. – have a double potential in dye removal and electricity generation. We inoculated the mixed electrogenic bacteria at a specific ratio and treated them with a triphenylmethane dye, Victoria blue R (VBR), to evaluate their electricity generation ability for the artificial and real wastewater. The results of the VBR shock-loading experiment indicated that the inoculated MFC could adapt to shock loading in 1–2 days and exhibited high removal efficiency (95–100%) for 100–800 mg L−1 VBR with a power density of 8.62 ± 0.10 to 34.81 ± 0.25 mW m−2. The selected electrogenic bacteria in the MFC could use VBR as only electron donor for power generation. The matrix effects of the real wastewater on VBR removal and electricity generation of MFC were insignificant. VBR degradation by the electrogenic bacteria involves a stepwise demethylation process to yield partially dealkylated VBR species. In addition, these results demonstrate the feasibility of inoculating culturable bacteria strains to develop an efficient MFC for purifying wastewater.
Lesions of the Orbitofrontal but not Medial Prefrontal Cortex Disrupt Conditioned Reinforcement in Primates

The ventromedial prefrontal cortex (PFC) is implicated in affective and motivated behaviors. Damage to this region, which includes the orbitofrontal cortex as well as ventral sectors of medial PFC, causes profound changes in emotional and social behavior, including impairments in certain aspects of decision making. One reinforcement mechanism that may well contribute to these behaviors is conditioned reinforcement, whereby previously neutral stimuli in the environment, by virtue of their association with primary rewards, take on reinforcing value and come to support instrumental action. Conditioned reinforcers are powerful determinants of behavior and can maintain responding over protracted periods of time in the absence of and potentially in conflict with primary reinforcers. It has already been shown that conditioned reinforcement is dependent on the amygdala, and because the amygdala projects to both the orbitofrontal cortex and the medial PFC, the present study determined whether conditioned reinforcement was also dependent on one or the other of these prefrontal regions. Comparison of the behavioral effects of selective excitotoxic lesions of the PFC in the common marmoset revealed that orbitofrontal but not medial PFC lesions disrupted two distinct measures of conditioned reinforcement: (1) acquisition of a new response and (2) sensitivity to conditioned stimulus omission on a second-order schedule. In contrast, the orbitofrontal lesion did not affect sensitivity to primary reinforcement as measured by responding on a progressive-ratio schedule and a home cage consumption test. Together, these findings demonstrate the critical and specific involvement of the orbitofrontal cortex but not the medial PFC in conditioned reinforcement.
Study of Local Trapping and STI Edge Effects on Charge-Trapping NAND Flash

Unlike the floating gate Flash device, charge-trapping (CT) devices store charges locally and are thus profoundly affected by non-uniform injection effect. The characteristics of a CT device are dominated by the local minimum-Vt region along the channel width. We have analyzed various STI structures including raised-STI, recessed-STI, and near-planar structures, and found that the program/erase characteristics are strongly impacted by the STI corner geometry due to local field enhancement (FE) and non-uniform injection effects. Moreover, both gm and S.S. vary during program/erase and thus increase programming/erasing complexity. The read disturb, program disturb, and retention characteristics are examined in detail. These conclusions apply to all CT devices.
The length–force behavior and operating length range of squid muscle vary as a function of position in the mantle wall

Hollow cylindrical muscular organs are widespread in animals and are effective in providing support for locomotion and movement, yet are subject to significant non-uniformities in circumferential muscle strain. During contraction of the mantle of squid, the circular muscle fibers along the inner (lumen) surface of the mantle experience circumferential strains 1.3 to 1.6 times greater than fibers along the outer surface of the mantle. This transmural gradient of strain may require the circular muscle fibers near the inner and outer surfaces of the mantle to operate in different regions of the length–tension curve during a given mantle contraction cycle. We tested the hypothesis that circular muscle contractile properties vary transmurally in the mantle of the Atlantic longfin squid, Doryteuthis pealeii. We found that both the length–twitch force and length–tetanic force relationships of the obliquely striated, central mitochondria-poor (CMP) circular muscle fibers varied with radial position in the mantle wall. CMP circular fibers near the inner surface of the mantle produced higher force relative to maximum isometric tetanic force, P0, at all points along the ascending limb of the length–tension curve than CMP circular fibers near the outer surface of the mantle. The mean ± s.d. maximum isometric tetanic stresses at L0 (the preparation length that produced the maximum isometric tetanic force) of 212±105 and 290±166 kN m−2 for the fibers from the outer and inner surfaces of the mantle, respectively, did not differ significantly (P=0.29). The mean twitch:tetanus ratios for the outer and inner preparations, 0.60±0.085 and 0.58±0.10, respectively, did not differ significantly (P=0.67). The circular fibers did not exhibit length-dependent changes in contraction kinetics when given a twitch stimulus. As the stimulation frequency increased, L0 was approximately 1.06 times longer than LTW, the mean preparation length that yielded maximum isometric twitch force. Sonomicrometry experiments revealed that the CMP circular muscle fibers operated in vivo primarily along the ascending limb of the length–tension curve. The CMP fibers functioned routinely over muscle lengths at which force output ranged from only 85% to 40% of P0, and during escape jets from 100% to 30% of P0. Our work shows that the functional diversity of obliquely striated muscles is much greater than previously recognized.
Prevalance of agenesis of palmaris longus muscle in gujarat population

Background: Palmaris longus muscle is one of the superficial slender muscles of forearm that act on the skin and distal digital webs. It has been described as a phylogenetically degenerate metacarpophalangeal joint flexor. It is harvested as a tendon graft in many surgical procedures. Palmaris longus muscle is a choice of muscle in cosmetic, plastic and reconstructive surgery. There are many studies on various ethnic groups of different regions. Aim: This prospective, observational and cross sectional study was conducted to determine the prevalence of unilateral and bilateral agenesis of Palmaris Longus and its association with sex and side of the limb in the Gujarat population of India. Materials and Methods: The clinical study was conducted on 474 subjects (273 males and 201 females) belonging to 18 – 25 years for agenesis of palmaris longus by various clinical techniques and the cadaveric study was conducted on 50 upper limbs of 25 cadavers of Gujarat region. Data was collected and analyzed by Chi-square test. Results: In clinical study total agenesis of palmaris longus muscle was seen in 67(13.08%) subjects out of whom 13.19% were males and 12.94% were females. Unilateral agenesis was seen in 38.71%, bilateral agenesis in 61.29%, right sided agenesis in 45.83% and left sided in 54.17%. In cadavers out of 50 upper limbs, Palmaris longus agenesis was seen in total 4 limbs in which 1 limb had bilateral agenesis and 2 left limbs had unilateral agenesis. Conclusions: Prevalence of palmaris longus agenesis is more common in males and unilateral agenesis is more common on left side.
A Re-examination of Question Classification

This paper presents a re-examiniation of previous work on machine learning techniques for questions classification, as well as results from new experiments. The results suggest that some of the work done in the field have yielded biased results. The results also suggest that Naive Bayes, Decision Trees and Support Vector Machines perform on par with each other when faced with actual users’ questions.
Lipoprotein(a) levels in relation to diabetic complications in patients with non‐insuIin‐dependent diabetes

Abstract. The relationship between serum levels of lipoprotein(a) (Lp(a)) and the presence of chronic diabetic complications was studied in 194 patients with non‐insulin‐dependent diabetes mellitus (NIDDM; 75 males, 119 females; age 66±11 years; duration of diabetes, 11 (range 1–35) years). They were taking various treatments (diet alone, oral hypoglycaemic agents and/or insulin). Metabolic status and prevalence of diabetic complications were assessed by detailed history, physical examination, laboratory analysis and ECG. Average metabolic control was moderate (HbAle, 8.2±1.7%). Median serum Lp(a) level was 183 U 1‐‐1 (range 8–2600 U I‐1), which was significantly higher than in control subjects of comparable age (median 101; range 8–1747 U I‐1; P<0.05), while HDL‐cholesterol levels were lower (1.14 ± 0.38 vs. 1.35 ± 0.35 mmol l‐1; P=0.001), and total cholesterol levels were comparable. No significant relation ships between diabetes treatment or metabolic control and Lp(a) levels were observed. In the quartile of patients with the highest Lp(a) levels. total cholesterol and triglycerides were slightly higher (P < 0.05), where as HDL‐cholesterol was not different. With increasing Lp(a) levels, higher prevalences of preproliferative retinopathy and of coronary artery disease (CAD) were observed, but not of the other complications. No relationship was found between the degree of albuminuria and Lp(a) levels. We conclude that in NIDDM patients, Lp(a) levels are elevated compared with non‐diabetic subjects, and that higher Lp(a) levels are associated with higher prevalences of CAD and of retinopathy.
Lethal model 2: the limits to growth revisited.

The author examines some major concerns about global economic growth from both theoretical and empirical points of view, using "the limits-to-growth debate as a reference point to understand the earlier debate about the limits to and perils of growth, and to provide some perspective about the newer debate about environmental threats. " He concludes that environmental and resource constraints on economic growth should be modest over the next 50 years and that economic growth is possible providing emphasis is given to "the importance of careful scientific and policy analysis and establishing or strengthening institutions that contain incentives that are compatible with the thoughtful balancing of long-run costs and benefits of social investments. "
Language Support for Distribution in CSCW Systems

Systems for Computer Supported Cooperative Work (CSCW) are demanding in their use of distributed systems infrastructure. CSCW systems typically require facilities such as group communication (multicast), object replication, and streamed, multi-party audio or video. The interaction mechanisms supported by mainstream tools like CORBA[19] and DCE[24] are low-level and limited to message passing or remote procedure call (RPC). While this is sufficient for information processing applications with simple client-server or three-tier communication requirements, it falls short of supporting the flexibility and complexity required by CSCW systems[5, 22, 14]. There are a number of research-oriented toolkits, for example GroupKit[23] and COAST[25], that support some of the required facilities for CSCW applications. These do not easily support extension or composition of facilities, however, because of their “toolkit” nature. In his recent PhD thesis[8], Paul Dourish suggests that correct approach to providing the necessary flexibility is through open implementation[15]. This technique requires an infrastructure to provide a representation of the underlying implementation that can be modified to suit application requirements, typically through reflection[16] in a programming language. With the suggestions of Dourish in mind, we are developing an executable language for describing the distribution aspects of CSCW systems. The language, Finesse, is based on the principles of the A1 p architecture model for distributed systems[4]. Its underlying semantics are described informally in [20], and a draft syntax has been defined[2]. This paper gives an overview of Finesse, its motivation, and its goals. A set of simple examples is provided in appendix A to give the flavour of the language and demonstrate the power of a language-based approach.
Some characteristics of gliomas managed at a Neurosurgery centre in Nigeria

Background: Gliomas are important primary brain tumours with varying prognosis. Aim: To study the histology characteristics of brain gliomas managed in a Neurosurgical centre in Nigeria. Materials and Methods: A retrospective analysis of prospectively recorded data of patients managed for intracranial gliomas at our Hospital for Neurosurgery, between year 2006 and 2015. Only the patients with conclusive histology diagnosis following surgery were analysed. Results: Glioma was 23.8% of the 252 histology-confirmed brain tumours. Male-to-female ratio was 1.4:1.0. Peak age at diagnosis was in the fifth decade of life. There was an increase in the frequency of diagnosis from seven (2006–2009) to 15 (2011 and 2012) and 39 patients managed (2013 and 2015). In sub-group analysis, grade IV tumour was the most common (34.6%) followed by grade II (30.7%), grade I (18.3%) and grade III (16.7%). Seven patients of grade II oligodendroglioma and one patient each of anaplastic oligodendroglioma, subependymal giant cell astrocytoma and astroblastoma were seen. The anatomical location of the tumour was the frontal lobe in 23.3% of patients followed by the parietal lobe in 16.7% of patients. The pre-operative Karnofsky score was ≥70% in 36.7% of the patients. Conclusion: Gliomas are more common brain tumours than were imagined. Most patients present relatively late and with advanced disease. High-grade gliomas seem to mostly affect the middle age population in the study environment with higher proportion of grade IV lesions.
Hasty decision-making in a variety of tasks: does it contribute to the development of delusions?

OBJECTIVES The finding that persons with delusions tend to jump-to-conclusions ( JTC) in the beads task has often been replicated. This study investigates whether hasty decision-making in the beads task is associated with hasty decisions in tasks with more relevance for everyday decision-making. Furthermore, it is hypothesized that hasty decisions in these tasks will be associated with subclinical delusional beliefs. DESIGN A correlational study. METHODS A sample of students (N=85) completed the beads task and three additional non-probabilistic decision-tasks. Subclinical delusional beliefs were assessed using the Peters et al. delusions inventory (PDI; Peters, Joseph, & Garety, 1999). RESULTS In support of the hypothesis, participants with hasty decisions in the beads task also made hasty decisions in two of the other tasks. Hasty decisions were only associated with higher subclinical delusional beliefs in one of the tasks (a letter recognition task). CONCLUSIONS Decision-making in the beads task can be generalized to decisions in other contexts. Other decision-making tasks may be more closely related to delusions than the beads task.
Genomic variations of the mevalonate pathway in porokeratosis

Porokeratosis (PK) is a heterogeneous group of keratinization disorders. No causal genes except MVK have been identified, even though the disease was linked to several genomic loci. Here, we performed massively parallel sequencing and exonic CNV screening of 12 isoprenoid genes in 134 index PK patients (61 familial and 73 sporadic) and identified causal mutations in three novel genes (PMVK, MVD, and FDPS) in addition to MVK in the mevalonate pathway. Allelic expression imbalance (AEI) assays were performed in 13 lesional tissues. At least one mutation in one of the four genes in the mevalonate pathway was found in 60 (98%) familial and 53 (73%) sporadic patients, which suggests that isoprenoid biosynthesis via the mevalonate pathway may play a role in the pathogenesis of PK. Significantly reduced expression of the wild allele was common in lesional tissues due to gene conversion or some other unknown mechanism. A G-to-A RNA editing was observed in one lesional tissue without AEI. In addition, we observed correlations between the mutations in the four mevalonate pathway genes and clinical manifestations in the PK patients, which might support a new and simplified classification of PK under the guidance of genetic testing. DOI: http://dx.doi. org/10.7554/eLife.06322. 001