Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleic Acids Research

We devised software tools to systematically investigate the contents and contexts of bacterial tRNA and tmRNA genes, which are known insertion hotspots for genomic islands (GIs). The strategy, based on MAUVE-facilitated multigenome comparisons, was used to examine 87 Escherichia coli MG1655 tRNA and tmRNA genes and their orthologues in E.coli EDL933, E.coli CFT073 and Shigella flexneri Sf301. Our approach identified 49 GIs occupying 1.7 Mb that mapped to 18 tRNA genes, missing 2 but identifying a further 30 GIs as compared with Islander [Y. Mantri and K. P. Williams (2004), Nucleic Acids Res., 32, D55–D58]. All these GIs had many strainspecific CDS, anomalous GC contents and/or significant dinucleotide biases, consistent with foreign origins. Our analysis demonstrated marked conservation of sequences flanking both empty tRNA sites and tRNA-associated GIs across all four genomes. Remarkably, there were only 2 upstream and 5 downstream deletions adjacent to the 328 loci investigated. In silico PCR analysis based on conserved flanking regions was also used to interrogate hotspots in another eight completely or partially sequenced E.coli and Shigella genomes. The tools developed are ideal for the analysis of other bacterial species and will lead to in silico and experimental discovery of new genomic islands.
Total knee arthroplasty: muscle impairments, functional limitations, and recommended rehabilitation approaches.

UNLABELLED The number of total knee arthroplasty (TKA) surgeries performed each year is predicted to steadily increase. Following TKA surgery, self-reported pain and function improve, though individuals are often plagued with quadriceps muscle impairments and functional limitations. Postoperative rehabilitation approaches either are not incorporated or incompletely address the muscular and functional deficits that persist following surgery. While the reason for quadriceps weakness is not well understood in this patient population, it has been suggested that a combination of muscle atrophy and neuromuscular activation deficits contribute to residual strength impairments. Failure to adequately address the chronic muscle impairments has the potential to limit the long-term functional gains that may be possible following TKA. Postoperative rehabilitation addressing quadriceps strength should mitigate these impairments and ultimately result in improved functional outcomes. The purpose of this paper is to describe these quadriceps muscle impairments and discuss how these impairments can contribute to the related functional limitations following TKA. We will also describe the current concepts in TKA rehabilitation and provide recommendations and clinical guidelines based on the current available evidence. LEVEL OF EVIDENCE Therapy, level 5.
Differential Treatment Response of Subtypes of Patients With Borderline Personality Organization, as Assessed With Theory-Driven Profiles of the Dutch Short Form of the MMPI: A Naturalistic Follow-Up Study

We investigated the validity of different subtypes of borderline personality organization (BPO) as assessed by theory-driven profiles of the Minnesota Multiphasic Personality Disorder (MMPI; Hathaway & McKinley, 1943) Dutch Short Form (DSFM; Eurelings-Bontekoe, Onnink, Williams, & Snellen, 2008) in a naturalistic follow-up study among 2,062 psychiatric outpatients who received 6 months of ambulatory treatment. Patients were assessed at intake (T1) and 6 months later (T2). At T2, both patients and therapists rated the level of improvement, using the Global Assessment of Improvement. Patients with the high-level BPO profile showed the largest increase in well-being and the largest decrease in severity of symptomatology, whereas severity of symptomatology and well-being of patients with psychotic BPO profiles did not change over time. Agreement between patients and therapists about improvement was good for the internalizing immature BPO and high-level BPO patients, but poor for the externalizing low-level BPO and narcissistic patients.
Giant negative electrocaloric effect in B-site non-stoichiometric (Pb0.97La0.02)(Zr0.95Ti0.05)1+yO3 anti-ferroelectric ceramics

ABSTRACT A negative electrocaloric effect (ECE) in B-site non-stoichiometric (Pb0.97La0.02)(Zr0.95Ti0.05)O3 antiferroelectric ceramics synthesized by the conventional solid-state reaction method is investigated via indirect and direct measurements. Temperature-dependent P-E hysteresis loops were measured. A giant negative electrocaloric temperature change of about 12.45 K was achieved. The results indicate that the antiferroelectric ceramics with non-stoichiometry modification could be a promising candidate for the applications in cooling devices. IMPACT STATEMENT Giant negative electrocaloric effect (NECE) was achieved in B-site non-stoichiometric PLZT2/95/5 ceramics, the NECE parameters are comparable or even larger than most of the reported bulk materials, making it attractive for cooling devices application. GRAPHICAL ABSTRACT
Matrix stiffness and serum concentration effects matrix remodelling and ECM regulatory genes of human bone marrow stem cells

The effects of mechanical stimulation of cell‐seeded collagen constructs on cell orientation, intracellular signalling and molecular responses have been widely reported. In this study we investigated in vitro the contractile responses of human bone marrow stem cells (HBMSCs) to increasing collagen gel substrate stiffness and their effect on extracellular matrix (ECM) regulatory genes. Human dermal fibroblasts (HDFs) were used as controls. Cells were cultured in 10% and 20% FCS and embedded in collagen constructs at a density of 1 million cells/ml collagen. Matrix stiffness was achieved by subjecting the constructs to three different strain regimes (0%, 5% and 10%), using a computer‐driven tensional culture force monitor (t‐CFM) capable of uniaxial loading. The contraction forces generated by the cells were quantified over 24 h. Molecular outputs were quantified using RT–PCR. HBMSCs significantly increased force generation to increasing serum concentration (i.e 10% to 20%). 10% FCS concentration significantly reduced contraction as pre‐strain stiffness was increased in HBMSCs and HDFs (0% > 5% > 10%). However, at 20% FCS HBMSCs generated similar peak force contraction at 24 h to 5% and 10% pre‐strain (0% = 5% = 10%). The ECM regulatory gene for MMP2 showed upregulation at 5% pre‐strain, but a 50% downregulation when pre‐strain was increased to 10%. MMP9 was upregulated at 5% pre‐strain and further upregulated at 10% pre‐strain. In designing tissue‐engineering solutions, predictable responses of cells, embedded within bio‐artificial matrices, to external mechanical forces are critical. To take into account the increasing stiffness of the matrix as increasing ECM is deposited, it would be necessary to take mechanical stimulation into account to determine predictable cellular responses. Copyright © 2008 John Wiley & Sons, Ltd.
The Evolution and Emergence of RNA Viruses

This impressive monograph by Edward Holmes opens with a quotation from La Peste, by Albert Camus: “Everyone knows that pestilences have a way of recurring in the world; yet somehow we find it hard to believe in ones that crash down on our heads from a blue sky. ” This apt quotation might lead the reader to believe that the evolution and emergence of RNA viruses in causing new diseases would be discussed, but in fact the book, as its title suggests, concentrates on how RNA viruses evolve and emerge at the molecular level, not how they cause disease. In addition to explaining what is currently known about the origins of RNA viruses, the book describes the mechanisms of RNA virus evolution, RNA virus quasispecies, and comparative genomics, as well as interesting new concepts, such as phylogeography. This term refers to the spatial movement of a phylogenetic species, which can be described in various ways (Holmes lists 5), two of which are the gravity model and the strong spatial subdivision model. In the former, patterns of transmission are driven by major population centers before moving out to smaller populations (influenza virus). In the spatial subdivision model, no clear evidence of migration among populations is presented (hepatitis C virus), and genomic diversity is partitioned into a series of clades (types and subtypes). Holmes argues persuasively that research in this area is limited by the size and detail of genome databases, combined with relevant epidemiologic and clinical information, such as precise geographic location, exact date of sampling, and transmission dynamics of the disease. The book is fully referenced and has a useful index, and I recommend it to those who have knowledge of and interest in the molecular biology of RNA viruses.
Endogenous Realignments and the Sustainability of a Target Zone

We examine the effects of endogenously determined realignment expectations in a model of a target zone with sluggish price adjustment. We allow these expectations to be based on a policy rule that generates an increasing probability of realignment as output moves away from full employment. We find that for realistic parameter values, even relatively small misalignments of the currency band lead to strongly skewed conditional distributions for the nominal exchange rate, thus generating pressures for realignment. We show that the reason for this is that the speed of adjustment in the absence of realignments is rather slow. Further, we find that the existence of an equilibrium path for the exchange rate depends on the responsiveness of realignment expectations to economic fundamentals. Paradoxically, higher credibility may increase the probability that a target zone will collapse. This feature of the model provides a possible explanation for the crisis within the exchange rate mechanism of the EMS. A policy of monetary accommodation to real shocks can alleviate the problem but severely constrains a country? s ability to pursue counterinflationary measures within the band.
Priming for tolerance and cohesion at replication forks

abstract Genome duplication is coupled with DNA damage tolerance (DDT) and chromatin structural changes. Recently we reported that mutations in Primase subunits or factors that bridge Polα/Primase with the replicative helicase, Ctf4, caused abnormal usage of DDT pathways, negatively influenced sister chromatid cohesion (SCC), and associated with increased fork reversal.1 We also found that cohesin, which is paradigmatic for SCC, facilitates recombination-mediated DDT. However, only the recombination defects of cohesin, but not of cohesion-defective Polα/Primase/Ctf4 mutants, were rescued by artificial tethering of sister chromatids. Genetic tests and electron microscopy analysis of replication intermediates made us propose that management of single-stranded DNA forming proximal to the fork is a critical determinant of chromosome and replication fork structure, and influences DDT pathway choice. Here we discuss the implications of our findings for understanding DDT regulation and cohesion establishment during replication, and outline directions to rationalize the relationship between these chromosome metabolism processes.
CAPLAN: An Accessible, Flexible and Scalable Semantification Architecture

The popularity of semantic information systems requires more data to be semantically prepared. However, the subsequent semantification process is still reserved for experts in Natural Language Processing. In this paper we define requirements for a state-of-the-art semantification architecture. Additionally we present a concept for a new semantification architecture meeting these requirements. Key strengths of the presented concepts are accessibility for non-experts, scalability and flexibility.
Phenylethylamine, a possible link to the antidepressant effects of exercise?

Objectives—To determine in this pilot study whether aerobic exercise affects phenylacetic acid concentration in the urine. Methods—Twenty healthy men provided 24 hour urine samples on two consecutive days for the determination of phenylacetic acid levels. Before and during day 1, subjects refrained from physical activity; on day 2 subjects ran on a treadmill at 70% of their maximal heart rate reserve (MHRR) for 30 minutes. Results—The 24 hour mean urinary concentration of phenylacetic acid was increased by 77% after exercise. Conclusion—As phenylacetic acid concentration in urine reflects phenylethylamine level, which is known to have antidepressant effects, phenylethylamine may be linked to the therapeutic effects of physical exercise on depression.
Quantifying the branching frequency of virtual filamentous microbes using fractal analysis

The productivity of an industrial fermentation process involving a filamentous microbe is heavily dependent on the morphological form adopted by the organism. The development of systems capable of rapidly and accurately characterizing morphology within a given process represents a significant challenge, as the complex phenotypes that are manifested are not easily quantified. Conventional parameters employed in these analyses are often of limited value, as they reveal little about the branching behavior of the organism; an important consideration given the demonstrated link between branching frequency and metabolite production. In this study, the influence of branching behavior on the spatial distribution of mycelia grown in silico is examined through fractal analysis. It is demonstrated that fractal dimension, quantified based on the frequency distribution of parameterized boundary curves, and lacunarity act as robust estimators of branching behavior. The analysis can, in theory, be applied to any morphological form, providing universally applicable process parameters for more complete data acquisition. Biotechnol. Bioeng. 2013; 110: 437–447. © 2012 Wiley Periodicals, Inc.
DNA sensing with nanopores in graphene nanoribbons

The information that can be extracted from DNA base sequences, is important for our understanding of biology, for insights in disease, and the way we practice medicine. The technology that one uses to determine DNA-base sequences is called ‘DNA sequencing’. A portable device that enables fast and accurate sequencing, can potentially greatly improve the quality of healthcare. Nanopores in graphene have potential for a new DNA sequencing technology that is superior to the current solutions.
Prognostic Value of Myocardial Damage in Patients With Sarcoidosis: Is Cardiac Magnetic Resonance What We Need?

Sarcoidosis is a granulomatous disease of unknown pathogenesis that can affect virtually any organ system. Cardiac involvement results in significant morbidity and mortality, with some studies reporting that cardiac involvement accounts for up to 25% of all deaths from sarcoidosis in the United States and more than half of all deaths in Japan.1–3 Many deaths seem to be arrhythmic in nature and are potentially preventable. For example, recent studies4,5 in patients with cardiac sarcoidosis (CS) and an implantable cardioverter-defibrillator show high rates of appropriate implantable cardioverter-defibrillator discharges (≈10%–15% per year for primary prevention patients), which are more than double that reported in large randomized trials of heart failure patients.6 See Article by Hulten et al Unfortunately, the diagnosis of cardiac involvement is difficult because the extent of disease is often limited and focal in nature. Necropsy studies have shown that patients with CS frequently have lesions that are small and patchy, leaving much of the myocardium uninvolved.1,7,8 Hence, although a positive endomyocardial biopsy is confirmatory, a negative biopsy cannot exclude CS because the false-negative rate may be as high as 80%. 9 Guidelines such as those from the Japanese Ministry of Health and Welfare (JMH)10 and, more recently, from the Heart Rhythm Society (HRS),11 have been published for the diagnosis of CS. Unfortunately, the recommendations rely heavily on expert opinion because the level of evidence is low. A particular limitation of the guidelines is that the diagnosis of CS requires the histological confirmation of sarcoidosis—either in the heart or outside the heart. Hence, in the absence of a positive myocardial biopsy, the guidelines do not provide a pathway to diagnose sarcoidosis confined to the heart. This is important because there is growing evidence that isolated CS …
Design of Concurrent Low-Noise Amplifier for Multi-Band Applications

A concurrent multi-band low-noise amplifler (LNA) for both WLAN and WiMAX applications covering 2.4{2.7GHz, 3.3{ 3.8GHz and 5.1{5.9GHz is mainly investigated. The proposed LNA consists of two cascaded common-source stages and employs stepped- impedance transformers and series and shunt feedback techniques to obtain good return loss, low noise and high linearity simultaneously. Test results show that the LNA features input and output return loss of 12dB, gain of 21dB, and noise flgure of 2dB across the three bands of operation, which are the state of the art among the counterparts.
THE IMPACT OF THE ALEXANDERWERK WP120 MILL UPPER MESH SIZE ON THE GRANULE PROPERTIES OF ALACTOSE/MICROCRYSTALLINE CELLULOSE PLACEBO FORMULATION

The continuous development of new active pharmaceutical ingredients (API) that are moisture sensitive, made roller compaction more popular, and thus encourages research into the different processing parameters whose modification may enhance the production of roller compactors. The Alexanderwerk WP120 is a roller compactor with an integrated two-stage mill that is used for small/medium scale batch manufacture. This study was carried out to determine the impact of upper mesh size of the integrated mill of the Alexanderwerk WP120 roller compactor on granule PSD, flow and compactability. The results showed that the upper mesh size may have a significant effect on PSD of lower solid fraction ribbon/wafer (≤ 0.65SF). However, these differences in PSD may not be sufficient to afford a significant change in bulk powder flow and compactability properties.
Rise and fall of a wolf population: genetic diversity and structure during recovery, rapid expansion and drastic decline

The grey wolves (Canis lupus) of Finland have had a varied history, with a period of rapid population expansion after the mid‐1990s followed by a decline with a current census size of about 140 wolves. Here, we investigate the impact of unstable population size and connectivity on genetic diversity and structure in a long‐term genetic study of 298 Finnish wolves born in 1995–2009 and genotyped for 17 microsatellite loci. During the initial recovery and prior to population expansion, genetic diversity was high (1995–1997: LD‐Ne = 67.2; Ho = 0.749; He = 0.709) despite a small census size and low number of breeders (Nc < 100; Nb < 10) likely reflecting the status of the Russian source population. Surprisingly, observed heterozygosity decreased significantly during the study period (t = −2.643, P = 0.021) despite population expansion, likely a result of an increase in inbreeding (FIS = 0.108 in 2007–2009) owing to a low degree of connectivity with adjacent Russian wolf population (m = 0.016–0.090; FST = 0.086, P < 0.001) and population crash after 2006. However, population growth had a temporary positive impact on Ne and number of family lines. This study shows that even strong population growth alone might not be adequate to retain genetic diversity, especially when accompanied with low amount of subsequent gene flow and population decline.
Mechanisms of host cell exit by the intracellular bacterium Chlamydia

The mechanisms that mediate the release of intracellular bacteria from cells are poorly understood, particularly for those that live within a cellular vacuole. The release pathway of the obligate intracellular bacterium Chlamydia from cells is unknown. Using a GFP-based approach to visualize chlamydial inclusions within cells by live fluorescence videomicroscopy, we identified that Chlamydia release occurred by two mutually exclusive pathways. The first, lysis, consisted of an ordered sequence of membrane permeabilizations: inclusion, nucleus and plasma membrane rupture. Treatment with protease inhibitors abolished inclusion lysis. Intracellular calcium signaling was shown to be important for plasma membrane breakdown. The second release pathway was a packaged release mechanism, called extrusion. This slow process resulted in a pinching of the inclusion, protrusion out of the cell within a cell membrane compartment, and ultimately detachment from the cell. Treatment of Chlamydia-infected cells with specific pharmacological inhibitors of cellular factors demonstrated that extrusion required actin polymerization, neuronal Wiskott–Aldrich syndrome protein, myosin II and Rho GTPase. The participation of Rho was unique in that it functioned late in extrusion. The dual nature of release characterized for Chlamydia has not been observed as a strategy for intracellular bacteria.
An image processing algorithm for a super high definition imaging scheme with multiple different-aperture cameras

Towards the development of a SHD (super high definition) image acquisition system, previously the authors developed the image-processing based approach with multiple cameras. Originally, in this approach, they used multiple cameras with the same pixel aperture, but in this case there needs to be severe limitations both in the arrangement of multiple cameras and in the configuration of the scene in order to guarantee the spatial uniformity of the resultant resolution. To overcome this difficulty completely, the authors have also previously presented the utilization of multiple cameras with different pixel apertures. The present paper develops a new, alternately iterative image processing algorithm available in the different aperture case. Experimental simulations clearly show that the alternately interactive algorithm behaves satisfactorily. <<ETX>>
Nitrous oxide emissions from municipal wastewater treatment.

Nitrous oxide (N 2 0) emissions from primary and secondary wastewater treatment processes were measured during spring and summer 1993 in Durham, NH. The most significant emissions occurred during secondary aeration. Dissolved N 2 0 generated as a result of denitrification during primary settling was stripped from the liquid during mechanical aeration. Emission factors derived from our field measurements included per capita emissions of 3.2 g of N 2 0 person -1 yr -1 and flow based emissions of 1.6 x 10 -6 of N 2 0 (L of wastewater) -1 .
Minimum phone error training of precision matrix models

Gaussian mixture models (GMMs) are commonly used as the output density function for large-vocabulary continuous speech recognition (LVCSR) systems. A standard problem when using multivariate GMMs to classify data is how to accurately represent the correlations in the feature vector. Full covariance matrices yield a good model, but dramatically increase the number of model parameters. Hence, diagonal covariance matrices are commonly used. Structured precision matrix approximations provide an alternative, flexible, and compact representation. Schemes in this category include the extended maximum likelihood linear transform and subspace for precision and mean models. This paper examines how these precision matrix models can be discriminatively trained and used on state-of-the-art speech recognition tasks. In particular, the use of the minimum phone error criterion is investigated. Implementation issues associated with building LVCSR systems are also addressed. These models are evaluated and compared using large vocabulary continuous telephone speech and broadcast news English tasks.