Miracle-dz/UniFAR-FTUs huggingface dataset:
Colonization Kinetics of Different Methicillin-Resistant Staphylococcus aureus Sequence Types in Pigs and Host Susceptibilities

ABSTRACT In this study we investigated the kinetics of colonization, the host susceptibility and transmissibility of methicillin-resistant Staphylococcus aureus (MRSA) after nasal treatment of pigs with three different MRSA strains of distinctive clonal lineages (sequence type 398 [ST398], ST8, and ST9), and origin in weaning piglets. The colonization dose of 5.0 × 108 CFU/animal was determined in preliminary animal studies. A total of 57 piglets were randomly divided into four test groups and one control group. Each of three test groups was inoculated intranasally with either MRSA ST8, MRSA ST9, or MRSA ST398. The fourth group was a mixture of animals inoculated with MRSA ST398 and noninoculated “sentinel” animals. Clinical signs, the nasal, conjunctival, and skin colonization of MRSA, fecal excretion, and organ distribution of MRSA, as well as different environmental samples were examined. After nasal inoculation with MRSA piglets of all four test groups showed no clinical signs of an MRSA infection. MRSA was present on the nasal mucosa, skin, and conjunctiva in all four test groups, including sentinel animals. Likewise, fecal excretion and internal colonization of MRSA ST8, ST9, and ST398 could be shown in each group. However, fecal excretion and the colonization rate of the nasal mucosa with MRSA ST9 were significantly lower in the first days after infection than in test groups infected with ST8 and ST398. The results of this study suggest differences in colonization potential of the different MRSA types in pigs. Furthermore, colonization of lymph nodes (e.g., the ileocecal lymph node) with MRSA of the clonal lineage ST398 was demonstrated.
Xenome—a tool for classifying reads from xenograft samples

Motivation: Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed. Results: We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets. Availability: Xenome is available for non-commercial use from http://www.nicta.com.au/bioinformatics Contact: tom.conway@nicta.com.au
Phase I Study of 68Ga-HER2-Nanobody for PET/CT Assessment of HER2 Expression in Breast Carcinoma

Human epidermal growth factor receptor 2 (HER2) status is one of the major tumor characteristics in breast cancer to guide therapy. Anti-HER2 treatment has clear survival advantages in HER2-positive breast carcinoma patients. Heterogeneity in HER2 expression between primary tumor and metastasis has repeatedly been described, resulting in the need to reassess HER2 status during the disease course. To avoid repeated biopsy with potential bias due to tumor heterogeneity, Nanobodies directed against HER2 have been developed as probes for molecular imaging. Nanobodies, which are derived from unique heavy-chain-only antibodies, are the smallest antigen-binding antibody fragments and have ideal characteristics for PET imaging. The primary aims were assessment of safety, biodistribution, and dosimetry. The secondary aim was to investigate tumor-targeting potential. Methods: In total, 20 women with primary or metastatic breast carcinoma (score of 2+ or 3+ on HER2 immunohistochemical assessment) were included. Anti-HER2-Nanobody was labeled with 68Ga via a NOTA derivative. Administered activities were 53–174 MBq (average, 107 MBq). PET/CT scans for dosimetry assessment were obtained at 10, 60, and 90 min after administration. Physical evaluation and blood analysis were performed for safety evaluation. Biodistribution was analyzed for 11 organs using MIM software; dosimetry was assessed using OLINDA/EXM. Tumor-targeting potential was assessed in primary and metastatic lesions. Results: No adverse reactions occurred. A fast blood clearance was observed, with only 10% of injected activity remaining in the blood at 1 h after injection. Uptake was seen mainly in the kidneys, liver, and intestines. The effective dose was 0.043 mSv/MBq, resulting in an average of 4.6 mSv per patient. The critical organ was the urinary bladder wall, with a dose of 0.406 mGy/MBq. In patients with metastatic disease, tracer accumulation well above the background level was demonstrated in most identified sites of disease. Primary lesions were more variable in tracer accumulation. Conclusion: 68Ga-HER2-Nanobody PET/CT is a safe procedure with a radiation dose comparable to other routinely used PET tracers. Its biodistribution is favorable, with the highest uptake in the kidneys, liver, and intestines but very low background levels in all other organs that typically house primary breast carcinoma or tumor metastasis. Tracer accumulation in HER2-positive metastases is high, compared with normal surrounding tissues, and warrants further assessment in a phase II trial.
A framework of psychological compensation in attention deficit hyperactivity disorder

The term compensation is widely used in the context of attention deficit hyperactivity disorder (ADHD), yet, it is neither defined nor theory driven. Adapting a model of psychological compensation (Bäckman and Dixon, 1992) to fit ADHD research is the aim of this review: we will (1) introduce the existing theoretical framework of psychological compensation, (2) discuss its applicability to ADHD and adapt the model to fit ADHD research, and (3) set up requirements for research on psychological compensation in ADHD. According to the framework psychological compensation can be inferred if a deficit (i.e., a mismatch between skill and environmental demand) is counterbalanced by the investment of more effort, the utilization of latent skills, or the acquisition of new skills. The framework has to be adapted because ADHD deficits are developmental and in individuals with ADHD compensation can appear independent of awareness of the deficit. A better understanding of psychological compensation in ADHD could foster diagnosis and interventions. Therefore, we suggest that future studies should follow a research design incorporating independent measures of deficit, compensation, and outcome as well as include individuals who compensate for their ADHD related deficits.
Enhancing public safety in primary care

Improving the safety record of the NHS is a national priority. This is not surprising, as recent research shows that up to 850 000 adverse events occur in hospitals every year.1 Up to 90 000 iatrogenic deaths may occur each year in hospitals in the United States,2 and the picture is likely to be similar in the United Kingdom. The landmark report To Err is Human has led to substantial investment in the US Agency for Health Research and Quality's safety unit.2 This was closely followed in the United Kingdom by the Department of Health reports An Organisation with a Memory and Building a Safer NHS, heralding the introduction of the National Patient Safety Agency. 3 4 Our understanding of the causes of iatrogenic adverse events in secondary care has increased substantially over the past decade, but the same cannot be claimed of primary care. In this paper, we consider public safety in primary care. What do we know about the main causes of harm to patients? To what extent are these preventable? How can we enhance public safety? We use these deliberations as a basis from which to propose a strategic response to the pressing challenge of improving the safety record of primary care. #### Summary points Safety is of increasing concern to the public and profession alike, but until now attention has been focused on secondary care Valuable research on safety has been conducted in primary care, and many other sources of information indicate where the major causes of harm might occur Safety is a major concern in four main areas—diagnosis, prescribing, communication, and organisational change Prescribing is the area about which most is known—3-5% of all prescriptions in primary care might cause problems, and one third of these can be classified as serious Of all adverse incidents …
Decreases in HCN mRNA expression in the hippocampus after kindling and status epilepticus in adult rats

Purpose: Studies in animal models and patients have implicated changes in hyperpolarization‐activated cyclic nucleotide‐gated cation channel (HCN) expression in the pathogenesis of temporal lobe epilepsy (TLE). However, the nature of HCN changes during the epileptogenic process and their commonality across different TLE models is unknown. Here HCN1 and HCN2 mRNA expression was quantitatively measured at different time points during epileptogenesis in two distinct animal models of TLE; the kainic acid (KA)‐induced status epilepticus (SE) and amygdala kindling models.
Geology and Age Constraints on the Origin of the Intrusion-Related, Sheeted Vein-Type Åkerberg Gold Deposit, Skellefte District, Sweden

The Early Proterozoic (~1.9 Ga) Skellefte mining district in northern Sweden hosts abundant base metal deposits, but there are also gold-only deposits. The Akerberg gold ore is unusual given the noted lack of alteration, a scarcity of sulfides and gold associated with thin (mm-cm wide) parallel quartz veins hosted in a gabbro. The gold content is positively correlated with the density of quartz veins, but gold often occurs between veins and also in parts of the gabbro where there is no veining. The gabbro is intruded by a granodiorite and associated pegmatite bodies, and U-Pb dating of zircon and baddeleyite suggest that these lithologies developed close in time at around 1.88 Ga ago. There are no primary inclusions in quartz veins, but different types of secondary aqueous inclusions occur. The Akerberg ore is interpreted as a sheeted vein complex, with veins constrained to tensional cracks induced when a granodioritic magma intruded the competent, sheet-like gabbro intrusion. It is suggested that unmixing of the felsic magma also produced pegmatite bodies and a gel-like melt which invaded fractures in the gabbro and deposited silica. In a comparison, the Akerberg ore shares many characteristics with the intrusion-related style of gold mineralizations.
Coarseness in Quantization for Stabilization of Linear Systems over Networks

We present an overview on the quantized control approach that was initiated by Elia and Mitter in the context of networked control. In particular, two recent extensions are presented where uncertainties in the channel and the plant are taken into consideration. The general problem setting is that the amount of communication is measured by a notion of coarseness in quantization, and we would like to find the coarsest quantizer for achieving stabilization. Numerical examples are provided to illustrate the differences among the quantized control schemes.
Coarse-to-fine low-rank structure-from-motion

We address the problem of deformable shape and motion recovery from point correspondences in multiple perspective images. We use the low-rank shape model, i.e. the 3D shape is represented as a linear combination of unknown shape bases. We propose a new way of looking at the low-rank shape model. Instead of considering it as a whole, we assume a coarse-to-fine ordering of the deformation modes, which can be seen as a model prior. This has several advantages. First, the high level of ambiguity of the original low-rank shape model is drastically reduced since the shape bases can not anymore be arbitrarily re-combined. Second, this allows us to propose a coarse-to-fine reconstruction algorithm which starts by computing the mean shape and iteratively adds deformation modes. It directly gives the sought after metric model, thereby avoiding the difficult upgrading step required by most of the other methods. Third, this makes it possible to automatically select the number of deformation modes as the reconstruction algorithm proceeds. We propose to incorporate two other priors, accounting for temporal and spatial smoothness, which are shown to improve the quality of the recovered model parameters. The proposed model and reconstruction algorithm are successfully demonstrated on several videos and are shown to outperform the previously proposed algorithms.
Long term use of lithium and factors associated with treatment response among patients with bipolar disorder.

BACKGROUND Lithium has been the gold standard in treating bipolar disorder. In recent years, the use of lithium seems to be diminished although it is well tolerated among the bipolar disorder patients. SUBJECTS AND METHODS This study aimed to evaluate the efficacy and tolerability of lithium as well as to determine factors associated with lithium response among patient with bipolar disorder. A retrospective study was done in a tertiary care hospital in Malaysia which included 47 bipolar disorder patients that were prescribed with lithium maintenance therapy in the time frame of January 2009 until December 2013. RESULTS Of all the baseline characteristics tested, only psychotic feature differentiated lithium monotherapy group and combination therapy group significantly (χ(2)=4.732, p=0.03). When compared to period before lithium maintenance, all outcome measures (i.e. annual relapse rate, proportion time spent ill and duration of mood episode) showed significant improvement after lithium maintenance in both treatment groups. Lithium discontinuation only occurred in five cases of adverse effects. Predominant depressive mood episode before lithium maintenance (OR=0.159, p=0.033) and first euthymic interval after lithium maintenance (OR=1.109, p=0.047) significantly predicted lithium response. DISCUSSION Lithium significantly reduced the frequency and time spent in relapse in patients with bipolar disorder. Predominant depressive mood polarity before lithium maintenance and longer first euthymic interval after lithium maintenance had been identified to predict lithium response significantly.
Investigation of Orthogonality of Multi-User Channels Using 73 GHz Statistical Channel Models

This paper focuses at the investigation of the degree of orthogonality or spatial separation of multiple users in a densely populated shopping mall scenario. For this purpose, we have used well known millimeter wave (mmWave) channel models and developed a statistical MIMO enabled channel simulator. We have analyzed the mutual orthogonality of the multi-user channels by changing the number of multipath clusters, base station (BS) antennas and inter antenna element distance. Our analysis shows that current channel models result in mmWave channels which are highly correlated in space and spatial separation of users is quite difficult. Increase in the number of multipath clusters, antenna spacing and the number of antenna elements reduce the spatial correlation of users but up to a certain extent and beyond that spatial separation is bottlenecked.
Neuronal Models for Studying Tau Pathology

Alzheimer's disease (AD) is the most frequent neurodegenerative disorder leading to dementia in the aged human population. It is characterized by the presence of two main pathological hallmarks in the brain: senile plaques containing β-amyloid peptide and neurofibrillary tangles (NFTs), consisting of fibrillar polymers of abnormally phosphorylated tau protein. Both of these histological characteristics of the disease have been simulated in genetically modified animals, which today include numerous mouse, fish, worm, and fly models of AD. The objective of this review is to present some of the main animal models that exist for reproducing symptoms of the disorder and their advantages and shortcomings as suitable models of the pathological processes. Moreover, we will discuss the results and conclusions which have been drawn from the use of these models so far and their contribution to the development of therapeutic applications for AD.
Retropharyngeal Lymph Node Metastasis in Nasopharyngeal Carcinoma: Prognostic Value and Staging Categories

Purpose: To investigate the incidence, prognostic value, and staging categories of retropharyngeal lymph node (RLN) metastasis in nasopharyngeal carcinoma (NPC). Experimental Design: We did a retrospective review of the data from 749 biopsy-proved nonmetastatic NPC patients. All patients had undergone contrast-enhanced computed tomography and had radiotherapy as their primary treatment. Results: The incidence of RLN metastasis was 51.5%. After adjusting for tumor (T) and node (N) classifications, a borderline significant difference of distant metastasis-free survival (DMFS) rates was observed between patients with or without RLN metastasis. In N0 disease, the presence of RLN metastasis was a significant independent predictor for overall survival (OS), loco-regional relapse-free survival, and DMFS in multivariate Cox modeling analysis. No significant difference was observed in all end points between patients with unilateral and bilateral RLN metastasis. The hazard ratios of death and distant failure for N0 with RLN metastasis were similar to N1. The survival curve of OS and DMFS for N0 disease with RLN metastasis had approximated that of N1 disease. The survival curve of OS for T1 disease with RLN metastasis was approximately the same as T2 disease. However, the survival curve of DMFS for T1 disease with RLN metastasis was approximately the same as in T3 disease. Conclusions: RLN metastasis has a tendency to affect the DMFS rates of patients with NPC. Retropharyngeal node involvement has a negative effect on the prognosis of N0 disease. RLN metastasis should be classified as N1.
Dpraodv: A Dyanamic Learning System Against Blackhole Attack in Aodv Based Manet

Security is an essential requirement in mobile ad hoc networks to provide protected communication between mobile nodes. Due to unique characteristics of MANETS, it creates a number of consequential challenges to its security design. To overcome the challenges, there is a need to build a multifence security solution that achieves both broad protection and desirable network performance. MANETs are vulnerable to various attacks, blackhole, is one of the possible attacks. Black hole is a type of routing attack where a malicious node advertise itself as having the shortest path to all nodes in the environment by sending fake route reply. By doing this, the malicious node can deprive the traffic from the source node. It can be used as a denial-of-service attack where it can drop the packets later. In this paper, we proposed a DPRAODV (Detection, Prevention and Reactive AODV) to prevent security threats of blackhole by notifying other nodes in the network of the incident. The simulation results in ns2 (ver2.33) demonstrate that our protocol not only prevents blackhole attack but consequently improves the overall performance of (normal) AODV in presence of black hole attack.
Single-molecule fluorescence resonance energy transfer reveals a dynamic equilibrium between closed and open conformations of syntaxin 1

Protein conformational transitions form the molecular basis of many cellular processes, such as signal transduction and membrane traffic. However, in many cases, little is known about their structural dynamics. Here we have used dynamic single-molecule fluorescence to study at high time resolution, conformational transitions of syntaxin 1, a soluble N-ethylmaleimide-sensitive factor attachment protein receptors protein essential for exocytotic membrane fusion. Sets of syntaxin double mutants were randomly labeled with a mix of donor and acceptor dye and their fluorescence resonance energy transfer was measured. For each set, all fluorescence information was recorded simultaneously with high time resolution, providing detailed information on distances and dynamics that were used to create structural models. We found that free syntaxin switches between an inactive closed and an active open configuration with a relaxation time of 0.8 ms, explaining why regulatory proteins are needed to arrest the protein in one conformational state.
Local production and imitations of Late Roman pottery from a well in the Roman necropolis of Cuma in Naples, Italy

Archaeological excavations performed in a funerary complex in Cuma (Campania region, Italy) unearthed excellently preserved common wares dated to the third century A.D. Archaeometric analyses were focused on Campanian pitchers, Aegean‐like cooking pots, and pyriform pitchers, the latter recorded for the first time in an Italian context. The local pitchers were manufactured with a high‐CaO clay (CaO = ca. 12 wt.%) and local volcanic temper, fired at ca. 800–850°C, as suggested by the presence of calcite. The Aegean‐like pots and the pyriform pitchers were made with low‐CaO clay (CaO ≤ 4.0 wt.%) mixed with a calcite‐bearing temper, along with volcanic and siliciclastic grains, and fired at 800–950°C. The comparison with raw materials inferred that local vessels were made with low‐CaO basinal clays which outcrop in the northern Campania region, and sands from the shoreline north of Cuma where carbonate, siliciclastic and volcanic phases mix together. Our results suggest that the Phlegraean Late Roman workshops produced their traditional vases along with imitations of Aegean‐like pottery. Thus, microregional production responded to a market demand requiring shapes and styles similar to imports from the eastern Mediterranean, with which commercial trade was still quite active.
ImagePlane: An Automated Image Analysis Pipeline for High-Throughput Screens Using the Planarian Schmidtea mediterranea

ImagePlane is a modular pipeline for automated, high-throughput image analysis and information extraction. Designed to support planarian research, ImagePlane offers a self-parameterizing adaptive thresholding algorithm; an algorithm that can automatically segment animals into anterior-posterior/left-right quadrants for automated identification of region-specific differences in gene and protein expression; and a novel algorithm for quantification of morphology of animals, independent of their orientations and sizes. ImagePlane also provides methods for automatic report generation, and its outputs can be easily imported into third-party tools such as R and Excel. Here we demonstrate the pipeline's utility for identification of genes involved in stem cell proliferation in the planarian Schmidtea mediterranea. Although designed to support planarian studies, ImagePlane will prove useful for cell-based studies as well.
Phylogenetic position of yeastlike endosymbionts of anobiid beetles

The Anobiid beetles Stegobium paniceum and Lasioderma serricorne possess the intracellular yeastlike symbionts Symbiotaphrina buchneri and Symbiotaphrina kochii, respectively, in the mycetome between the foregut and midgut. The nucleotide sequences of the small-subunit rRNA-encoding genes of the symbionts were determined for phylogenetic analysis. Five group I introns were found in the small-subunit rRNA-encoding genes of S. buchneri, but S. kochii lacked introns. The phylogenetic position of both symbionts was close to the class Discomycetes, which is a paraphyletic group. The two symbionts formed a monophyletic group distinct from the other major lineages. Both appear to have parted from other filamentous fungi during the early radiation of the euascomycetes and to have later become obligatory partners of the beetles.