Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and taxonomic characterization of Bordetella pseudohinzii sp. nov. isolated from laboratory-raised mice

Bordetella hinzii is known to cause respiratory disease in poultry and has been associated with a variety of infections in immunocompromised humans. In addition, there are several reports of B. hinzii infections in laboratory-raised mice. Here we sequenced and analysed the complete genome sequences of multiple B. hinzii-like isolates, obtained from vendor-supplied C57BL/6 mice in animal research facilities on different continents, and we determined their taxonomic relationship to other Bordetella species. The whole-genome based and 16S rRNA gene based phylogenies each identified two separate clades in B. hinzii, one was composed of strains isolated from poultry, humans and a rabbit whereas the other clade was restricted to isolates from mice. Distinctly different estimated DNA–DNA hybridization values, average nucleotide identity scores, gene content, metabolic profiles and host specificity all provide compelling evidence for delineation of the two species, B. hinzii – from poultry, humans and rabbit – and Bordetella pseudohinzii sp. nov. type strain 8-296-03T (=NRRL B-59942T=NCTC 13808T) that infect mice.
Acoustic phonetic properties of mid vowels in New Caledonian French

This paper investigates production of the mid vowels /e, ɛ, ø, œ, o, ɔ/ by four speakers of New Caledonian French (NCF). Formant and durational properties of these vowels are examined with respect to the type of syllable in which they occur. Results point to general adherence to the loi de position in NCF, such that the close-mid vowels occur in open syllables and the open-mid vowels occur in closed ones. There is, however, interspeaker variation concerning the realization of open syllable /ɛ/. There is also some evidence of /ɔ/-centralization in NCF, and of phonetically higher productions of /e/ and /o/ relative to other varieties.
Dynamics of Export Market Entry and Exit

We examine the process of internationalisation of firms, contributing to the knowledge on the factors behind a successful entry and operation in the export markets using duration analysis. Rich longitudinal microlevel data on Finnish manufacturing plants allow an indepth analysis of the life cycle of exporting plants over a time span of up to 25 years. In the first part of the analysis, we focus on the factors that explain the duration of time until entering plants start to export. The second part of the study concentrates on the duration of time until exit from the export markets. Our special focus is on the effects of foreign ownership, human capital and industry spillovers on export market entry and exit.
Factors stimulating riboflavin produced by Lactobacillus plantarum CRL 725 grown in a semi‐defined medium

Riboflavin (vitamin B2) is one of the B‐group water‐soluble vitamins and is essential for energy metabolism of the cell. The aim of this study was to determine factors that affect riboflavin production by Lactobacillus (L.) plantarum CRL 725 grown in a semi defined medium and evaluate the expression of its rib genes. The factors found to enhance riboflavin production in this medium were incubation at 30 °C, and the addition of specific medium constituents, such as casamino acids (10 g L−1), guanosine (0.04 g L−1), and sucrose as carbon source (20 g L−1). In these conditions, higher riboflavin concentrations were directly associated with significant increases in the expression of ribA, ribB, and ribC genes. The culture conditions defined in this work and its application to a roseoflavin resistant mutant of L. plantarum allowed for a sixfold increase in riboflavin concentrations in our semi‐defined medium which were also significantly higher than those obtained previously using the same strain to ferment soymilk. These conditions should thus be evaluated to increase vitamin production in fermented foods.
A Need for Standardized Definitions for Clinical Studies of Pneumocystis

THE fungal pathogen Pneumocystis jirovecii, formerly known as Pneumocystis carinii f. sp. hominis, is the cause of Pneumocystis pneumonia (PcP) in humans (Redhead et al. 2006). Pneumocystis pneumonia is a major cause of morbidity and mortality in patients immunocompromised by human immunodeficiency virus (HIV) infection, malignancy, transplantation and in those receiving therapeutic immunosuppression (Cisneros et al. 1998; Fetic et al. 2005; Morris et al. 2004a). While there have been major advances in our understanding of the basic biology of Pneumocystis, uncertainties remain in regard to the mode of acquisition of infection by the human host, the (person to person) transmissibility of the organism, and the mechanisms of development of drug resistance. The study of P. jirovecii infection is hampered by the lack of a sustainable in vitro culture method. Human immunodeficiency virus-associated PcP remains a significant clinical problem with attendant morbidity and mortality in those countries without access to potent combination antiretroviral therapy (CART) or prophylaxis against PcP. However, in developed countries the availability of CART in addition to use of PcP prophylaxis means that the incidence of PcP has fallen steeply among those living with HIV infection. This means that individual institutions or groups of institutions may be unable to explore unanswered clinically important questions and collaborations between multiple centers may be needed to address these issues (Huang, Morris, and Beard 2001). It has become increasingly apparent that individual centers, when describing and defining their patients’ clinical status, method of laboratory diagnosis, and response to therapy and outcome may use different criteria. These variations in study design and outcome make more difficult the interpretation of individual studies and hamper their synthesis into the ‘‘body of knowledge’’ of human Pneumocystis infection. Following the meetings at the International Workshops on Opportunistic Protists held in Cincinnati in 2001 (IWOP-7), the American Thoracic Society (ATS) International Conference held in Atlanta in 2002, and the ATS-sponsored workshop on ‘‘Pneumocystis Pneumonia: Recent Advances and Future Directions’’ held in San Diego in 2005, a further ‘‘ad hoc’’ meeting was held in 2006 during IWOP-9 meetings in Lisbon, Portugal. Arising from this latter meeting it was apparent that there were several areas of uncertainty in our understanding of the human infection with Pneumocystis. As an outcome from this ‘‘ad hoc’’ meeting, which was attended by 25 individuals who are actively involved in basic science, laboratory, and clinical research, this paper highlights some of the current areas of uncertainty and the critical need for standardized definitions for clinical studies of Pneumocystis. SELECTED AREAS OF UNCERTAINTY
Scientific and ethical issues in the use of placebo controls in clinical trials.

The experience of being a subject in a clinical trial may include such activities as multiple clinic visits, research-subject interactions, the perfor­ mance of diagnostic tests, the taking of test medications, and many other measurable and unmeasurable features. All of these aspects may contribute to improvement in the signs and symptoms of the disease process being studied. The object of a clinical trial is to estimate the true effect of a therapeutic intervention. To accomplish this, one must be able to distinguish the effectiveness of the test therapy from the effect of simply being in a trial. Placebos are used in randomized trials with the intention of providing a control group whose experience in the trial is as similar as possible to that of the investigational group, except for the presence of the active ingredient(s) being tested. Placebos have long been used as therapeutic agents, generally without the knowledge and cooperation of the patient. The primary difference in the use of placebos in the context of a randomized trial is that both researcher and subject are aware that the subject has a chance of receiving a placebo instead of the test intervention. Much of our knowledge of placebos as
Cell death in cultured human Saos2 osteoblasts exposed to low‐density lipoprotein

Osteoporosis (OP) and atherosclerotic‐cardiovascular diseases (and possibly dementia) constitute emerging age‐related co‐morbidity states that might share risk factors. Blood‐born lipids, like LDL involved in atherosclerosis and apolipoprotein‐E4 (ApoE4) involved in dementia, may also be implicated in development of OP. We examined osteoblast cell lines as a culture model for OP by exposure to lipoproteins. ApoE expression in Saos2 and U2OS osteoblasts was confirmed by PCR. ApoE4 did decrease cell counts relatively to ApoE3, especially in Saos2 cells in which it was less selective for cells with higher alkaline phosphatase (ALP, an osteoblast marker) activity than ApoE3. This associates with ApoE4, being a risk factor for both dementia and OP. Saos2, but not U2OS, showed a decrease in cell counts after 48 h exposure to native LDL (NLDL). Both cell lines had decreased cell counts already after 24 h when exposed to oxidized‐LDL (OxLDL) for which Saos2 also showed a higher sensitivity than U2OS. Exposure of Saos2 to both, OxLDL at low concentration (5 μg/ml) and NLDL revealed a shrunken size cell fraction of 17–23% on the fluorescence‐activated cell sorter (FACS) analysis. Such shrunken cell fraction was not seen when Saos2 cells were exposed to 50 μg/ml of OxLDL or to OxLDL combined with 10 nM dexamethasone (DEX, a stimulator of osteoprogenitor differentiation). DEX treatment has lysed the cells earlier than 24 h post exposure and has selected more resistant cells that did not show apoptotic shrinkage in the FACS analysis done after 24 h. We interpret this as a failure to detect the apoptotic cell fraction due to their lysis prior to the FACS analysis. Western blots performed at different time points (10 min, 30 min, 4 h, 24 h, and 48 h) under OxLDL + DEX revealed a fall in the positive regulator of pp60Src‐kinase phosphotyrosine (pY)418 relative to the DEX controls during the first 4 h. This is consistent with DEX osteogenic induction, known to be negatively regulated by c‐Src, although the pY418/pY529 ratios (negative/positive kinase regulation) fell only at the 10 min time point. Contrarily the pY418/pY529 ratio increased, relative to untreated controls, under 5 μg/ml and 50 μg/ml of NLDL at the 4 h time point and under 50 μg/ml NLDL only at the 10 min time point, being consistent with the ability of a higher dose of LDL to antagonize osteoblast differentiation. This could be even more acceptable if the NLDL would have become minimally oxidized during its long purification procedure. Under NLDL, the Bcl‐2/Bax ratio was pro‐apoptotic at 10 min, 30 min, and 4 h only under 50 μg/ml, whereas under OxLDL + DEX it was pro‐apoptotic only after 4 h suggesting that additional pathways contribute to cell death. These results indicate that lipid effects on human osteoblast lines in culture may be used as a model to identify molecular targets shared between OP and atherosclerosis for intervention in this co‐morbidity. J. Cell. Biochem. 90: 42–58, 2003. © 2003 Wiley‐Liss, Inc.
PROSPECT II: protein structure prediction program for genome-scale applications.

A new method for fold recognition is developed and added to the general protein structure prediction package PROSPECT (http://compbio.ornl.gov/PROSPECT/). The new method (PROSPECT II) has four key features. (i) We have developed an efficient way to utilize the evolutionary information for evaluating the threading potentials including singleton and pairwise energies. (ii) We have developed a two-stage threading strategy: (a) threading using dynamic programming without considering the pairwise energy and (b) fold recognition considering all the energy terms, including the pairwise energy calculated from the dynamic programming threading alignments. (iii) We have developed a combined z-score scheme for fold recognition, which takes into consideration the z-scores of each energy term. (iv) Based on the z-scores, we have developed a confidence index, which measures the reliability of a prediction and a possible structure-function relationship based on a statistical analysis of a large data set consisting of threadings of 600 query proteins against the entire FSSP templates. Tests on several benchmark sets indicate that the evolutionary information and other new features of PROSPECT II greatly improve the alignment accuracy. We also demonstrate that the performance of PROSPECT II on fold recognition is significantly better than any other method available at all levels of similarity. Improvement in the sensitivity of the fold recognition, especially at the superfamily and fold levels, makes PROSPECT II a reliable and fully automated protein structure and function prediction program for genome-scale applications.
Trapping noctuid moths with synthetic floral volatile lures

Male and female noctuid moths were collected from plastic bucket traps that were baited with different synthetic floral chemicals and placed in peanut fields. Traps baited with phenylacetaldehyde, benzyl acetate, and a blend of phenylacetaldehyde, benzyl acetate, and benzaldehyde collected more soybean looper moths, Pseudoplusia includens (Walker), than benzaldehyde‐baited or unbaited traps. Females comprised over 67% of the moths captured and most were mated. At peak capture, over 90 male and female moths per night were collected. In another experiment, phenylacetaldehyde delivered in plastic stoppers attracted more P. includens moths than traps baited using other substrates, but this chemical delivered in wax attracted more velvetbean caterpillar moths (Anticarsia gemmatalis Hübner). Other noctuid male and female moths collected included Agrotis subterranea (F.), Argyrogramma verruca (F.), Helicoverpa zea (Boddie), and several Spodoptera species. Aculeate Hymenoptera were collected in large numbers, especially in traps baited with phenylacetaldehyde delivered from stoppers.
Proteome profiling of vitreoretinal diseases by cluster analysis

Vitreous samples collected in retinopathic surgeries have diverse properties, making proteomics analysis difficult. We report a cluster analysis to evade this difficulty. Vitreous and subretinal fluid samples were collected from 60 patients during surgical operation of non‐proliferative diabetic retinopathy, proliferative diabetic retinopathy, proliferative vitreoretinopathy, and rhegmatogenous retinal detachment. For controls, we collected vitreous fluid from patients of idiopathic macular hole, epiretinal, and from a healthy postmortem donor. Proteins from these samples were subjected to quantitative proteomics using two‐dimensional gel electrophoresis. We selected 105 proteins robustly expressed among ca. 400 protein spots and subjected them to permutation test. By using permutation test analysis we observed unique variations in the expression of some of these proteins in vitreoretinal diseases when compared to the control and to each other: (i) the levels of inflammation‐associated proteins such as alpha1‐antitrypsin, apolipoprotein A4, albumin, and transferrin were significantly higher in all four types of vitreoretinal diseases, and (ii) each vitreoretinal disease elevated a unique set of proteins, which can be interpreted based on the pathology of retinopathy. Our protocol will be effective for the study of protein expression in other types of clinical samples of diverse properties.
Different Surgical Approach to Sacculer Renal Artery Aneurysm : Case Report

Renal artery aneurysms are rare and are often detected incidentally in examinations for different purposes. Fifty-six -year-old female patient , intraarterial digital substracting saccular in 25 mm × 20 mm originating from the renal artery angiography revealed the presence of an aneurysm. Midline aneurysm was excised by laparotomy. Saphena 2 cm × 2 cm patch and 6.0 prolene form over and over was implanted with sewing technique. Cross clamp time was 13 minutes. Successful surgical correction is possible with almost complete intervention. The repair technique was safe with patchplasty. We believe that a successful alternative surgical option of saphneouse ptachplasty technigue.
Temporal trends in deep ocean redfield ratios.

The Redfield ratio [carbon:nitrogen:phosphorus (C:N:P)] of particle flux to the deep ocean is a key factor in marine biogeochemical cycling. Changes in oceanic carbon sequestration have been linked to variations in the Redfield ratio on geological time scales, but this ratio generally is assumed to be constant with time in the modern ocean. However, deep-water Redfield ratios in the northern hemisphere show evidence for temporal trends over the past five decades. The North Atlantic Ocean exhibits a rising N:P ratio, which may be related to increased deposition of atmospheric nitrous oxides from anthropogenic N emissions. In the North Pacific Ocean, increasing C:N and C:P ratios are accompanied by rising remineralization rates, which suggests intensified export production. Stronger export of carbon in this region may be due to enhanced bioavailability of aeolian iron. These findings imply that the biological part of the marine carbon cycle currently is not in steady state.
ECMTADR: Energy Conservative Multitier Architecture with Data Reduction for Cluster-Based Wireless Sensor Networks

Regarding the energy shortage problem of wireless sensor networks (WSNs), various schemes and protocols are proposed to prolong the network lifetime. Data communication is undoubtedly the most important determinant for this energy scarce network type. In this paper, we propose a sophisticated architecture comprising data reduction, load balance, and topology control. Data reduction is ensured by the parameter spatial correlation proximity range (SCPR) that can be adjusted statically at the setup phase or dynamically revised depending on the necessities in the network. Four-layer virtual architecture is applied for implementing topology control. Furthermore, network area is partitioned into fixed-size hexagonal clusters. Depending on the regions in which the clusters take place, cluster heads (CHs) are elected from the respective subregions of the clusters. Load balance is achieved by considering residual energies and distances to the sink during both CH election and data transmission stages. Aggregated data in each cluster is transmitted towards the sink by using a load balancing single-hop intercluster routing protocol instead of direct transmission as offered in LEACH. Simulation results demonstrate that the proposed architecture ECMTADR shows almost 50% better performance in terms of energy conservation and network lifetime when it is compared to LEACH and HEED.
$8\times 8$  Flexible Wavelength Cross-Connect for CDC ROADM Application

We propose and demonstrate an 8 × 8 flexible wavelength cross-connect (FWXC) switch that supports flex-grid wavelength assignment switching with contentionless feature. The developed switch is characterized for insertion loss, passband, frequency-tuning granularity, and port crosstalk. Based on the FWXC, we experimentally demonstrate a novel ultracompact colorless/directionless/contentionless-reconfigurable optical add drop multiplexer supporting four directions. Mixed 10G/40G/100G signals on add, drop, and express paths are tested. The optical signal-to-noise ratio (OSNR) penalties are observed <;0.25 dB for all the cases.
Yeast Shuttling SR Proteins Npl3p, Gbp2p, and Hrb1p Are Part of the Translating mRNPs, and Npl3p Can Function as a Translational Repressor

ABSTRACT A major challenge in current molecular biology is to understand how sequential steps in gene expression are coupled. Recently, much attention has been focused on the linkage of transcription, processing, and mRNA export. Here we describe the cytoplasmic rearrangement for shuttling mRNA binding proteins in Saccharomyces cerevisiae during translation. While the bulk of Hrp1p, Nab2p, or Mex67p is not associated with polysome containing mRNAs, significant amounts of the serine/arginine (SR)-type shuttling mRNA binding proteins Npl3p, Gbp2p, and Hrb1p remain associated with the mRNA-protein complex during translation. Interestingly, a prolonged association of Npl3p with polysome containing mRNAs results in translational defects, indicating that Npl3p can function as a negative translational regulator. Consistent with this idea, a mutation in NPL3 that slows down translation suppresses growth defects caused by the presence of translation inhibitors or a mutation in eIF5A. Moreover, using sucrose density gradient analysis, we provide evidence that the import receptor Mtr10p, but not the SR protein kinase Sky1p, is involved in the timely regulated release of Npl3p from polysome-associated mRNAs. Together, these data shed light onto the transformation of an exporting to a translating mRNP.
DNAJB6 Induces Degradation of β-Catenin and Causes Partial Reversal of Mesenchymal Phenotype*

We showed that expression of MRJ (DNAJB6) protein is lost in invasive ductal carcinoma, and restoration of MRJ(L) restricts malignant behavior of breast cancer and melanoma cells. However, the signaling pathways influenced by MRJ(L) are largely unknown. Our observations revealed that MRJ(L) expression causes changes in cell morphology concomitant with down-regulation of several mesenchymal markers, viz. vimentin, N-cadherin, Twist, and Slug, and up-regulation of epithelial marker keratin 18. Importantly, MRJ(L) expression led to reduced levels of β-catenin, an epithelial mesenchymal transition marker, and a critical player in the Wnt pathway. We found that MRJ(L) up-regulates expression of DKK1, a well known Wnt/β-catenin signaling inhibitor, that causes degradation of β-catenin. Re-expression of DNAJB6 alters the Wnt/β-catenin signaling in cancer cells, leading to partial reversal of the mesenchymal phenotype. Thus, MRJ(L) may play a role in maintaining an epithelial phenotype, and inhibition of the Wnt/β-catenin pathway may be one of the potential mechanisms contributing to the restriction of malignant behavior by MRJ(L).
Research productivity in neurosurgery: trends in globalization, scientific focus, and funding.

OBJECT While research is important for the survival, growth, and expansion of neurosurgery, little work has been done to quantify the status and trends of neurosurgical publications. The purpose of this bibliometric study was to quantitatively analyze trends in neurosurgical publications, including changes in worldwide productivity, study methodology, subspecialty topic, and funding. METHODS This was a retrospective bibliometric study using MEDLINE to record all publications between 1996 and 2009 by first authors affiliated with neurosurgical departments. Country of origin, MEDLINE-defined methodology, study topic, and funding sources (for US articles) were recorded. Linear regression was used to derive growth rates. RESULTS Total articles numbered 53,425 during the study period, with leading global contributors including the US with 16,943 articles (31.7%) and Japan with 10,802 articles (20.2%). Countries demonstrating rapid growth in productivity included China (121.9 ± 9.98%/year, p < 0.001), South Korea (50.5 ± 4.7%/year, p < 0.001), India (19.4 ± 1.8%/year, p < 0.001), and Turkey (25.3 ± 2.8%/year, p < 0.001). While general research articles, case reports, and review articles have shown steady growth since 1996, clinical trials and randomized controlled trials have declined to 2004 levels. The greatest overall subspecialty growth was seen in spine surgery. Regarding funding, relative contribution of National Institutes of Health (NIH)-funded publications decreased from 30.2% (290 of 959) to 22.5% (356 of 1229) between 1996 and 2009. CONCLUSIONS Neurosurgical publications demonstrate continued increases in productivity as well as in global expansion, although US contributions remain dominant. Two challenges that the neurosurgical community is facing include the preponderance of case reports and review articles and the relative decline in NIH funding for US neurosurgical publications, as productivity has outpaced government financial support.