Miracle-dz/UniFAR-FTUs huggingface dataset:
Individual Maize Chromosomes in the C3 Plant Oat Can Increase Bundle Sheath Cell Size and Vein Density1[W][OA]

C4 photosynthesis has evolved in at least 66 lineages within the angiosperms and involves alterations to the biochemistry, cell biology, and development of leaves. The characteristic “Kranz” anatomy of most C4 leaves was discovered in the 1890s, but the genetic basis of these traits remains poorly defined. Oat × maize addition lines allow the effects of individual maize (Zea mays; C4) chromosomes to be investigated in an oat (Avena sativa; C3) genetic background. Here, we have determined the extent to which maize chromosomes can introduce C4 characteristics into oat and have associated any C4-like changes with specific maize chromosomes. While there is no indication of a simultaneous change to C4 biochemistry, leaf anatomy, and ultrastructure in any of the oat × maize addition lines, the C3 oat leaf can be modified at multiple levels. Maize genes encoding phosphoenolpyruvate carboxylase, pyruvate, orthophosphate dikinase, and the 2′-oxoglutarate/malate transporter are expressed in oat and generate transcripts of the correct size. Three maize chromosomes independently cause increases in vein density, and maize chromosome 3 results in larger bundle sheath cells with increased cell wall lipid deposition in oat leaves. These data provide proof of principle that aspects of C4 biology could be integrated into leaves of C3 crops.
S CENARIOS OF FUTURE LUNG CANCER INCIDENCE BY EDUCATIONAL LEVEL : MODELLING STUDY IN D ENMARK

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Scenarios of future lung cancer incidence by educational level: Modelling study in Denmark. Gwenn Menvielle, Isabelle Soerjomataram, Esther De Vries, Gerda Engholm, Jan Barendregt, Jan Willem Coebergh, Anton Kunst
Evaluation of a New Etest Vancomycin-Teicoplanin Strip for Detection of Glycopeptide-Intermediate Staphylococcus aureus (GISA), in Particular, Heterogeneous GISA

ABSTRACT Glycopeptide-intermediate Staphylococcus aureus (GISA) and, in particular, heterogeneous GISA (hGISA) are difficult to detect by standard MIC methods, and thus, an accurate detection method for clinical practice and surveillances is needed. Two prototype Etest strips designed for hGISA/GISA resistance detection (GRD) were evaluated using a worldwide collection of hGISA/GISA strains covering the five major clonal lineages. A total of 150 strains comprising 15 GISA and 60 hGISA strains (defined by population analysis profiles-area under the curve [PAP-AUC]), 70 glycopeptide-susceptible S. aureus (GSSA) strains, and 5 S. aureus ATCC reference strains were tested. For standardized Etest vancomycin (VA) MIC testing, the modified Etest macromethod with VA and teicoplanin (TP) strips tested with a heavier inoculum using brain heart infusion agar (BHI) and two glycopeptide screening agar plates (6 μg/ml VA/BHI and 5 μg/ml Mueller-Hinton agar [MHA]) were tested in parallel with the two new Etest GRD strips: a VA 32 (0.5-μg/ml)-TP 32 (0.5-μg/ml) double-sided gradient (E-VA/TP) with one prototype overlaid with a nutrient (E-VA/TP+S) to enhance the growth of hGISA. The Etest GRD strips were tested with a standard 0.5-McFarland standard inoculum using MHA and MHA plus 5% blood (MHB) and were read at 18 to 24 and 48 h. The interpretive MIC cutoffs used for the new Etest GRD strips at 24 and 48 h were as follows: for GISA, TP or VA, ≥8, and a standard VA MIC of ≥6; for hGISA, TP or VA, ≥8, and a standard VA MIC of ≤4. The results on MHB at 48 h showed that E-VA/TP+S had high specificity (94%) and sensitivity (95%) in comparison to PAP-AUC and was able to detect all GISA (n = 15) and 98% of hGISA (n = 60) strains. In contrast, the glycopeptide screening plates performed poorly for hGISA. The new Etest GRD strip (E-VA/TP+S), utilizing standard media and inocula, is a simple and acceptable tool for detection of hGISA/GISA for clinical and epidemiologic purposes.
Treatment of Dermatofibroma Sarcoma Protuberans Using Modified Mohs Micrographic Surgery: No Recurrences and Smaller Defects

OBJECTIVES The purpose of this study was to evaluate the use of modified Mohs micrographic surgery (MMS) for dermatofibromasarcoma protuberans (DFSP) in a single institution by a single surgeon. METHODS The authors conducted a retrospective analysis of 25 patients with DFSP who were treated with modified MMS over the past 19 years at Scripps Clinic. RESULTS Of the 25 patients treated with modified MMS for DFSP, there were no identifiable recurrences. The mean follow-up time was 101 months. The defect sizes of DFSP lesions treated by modified MMS are smaller than if the lesions had been treated with the standard wide local excision (WLE) margins of 3 cm. LIMITATIONS This is a retrospective analysis using the data of one surgeon. Five of the 25 patients were not examined in our office. Not all patients had 5-year follow-up. There were no cases of the fibrosarcomatous variant. CONCLUSION Our data support the growing literature that modified MMS achieves excellent local control for DFSP with a possible benefit of smaller defects when compared with treatment with WLE.
Perceived Acceptability of Implementing Marker-Assisted Selection in the Forests of British Columbia

The forest sector in British Columbia (BC) has faced a number of challenges over the past decade. In response to some of those challenges, the government has invested in forest genomic tools. Marker-assisted selection (MAS) is a biotechnological tool that flags desired traits on the genome. This tool may assist tree breeders with the early selection of preferred genotypes, reducing the breeding cycle and more accurately and efficiently selecting for improved qualities. However, there is a poor understanding of the perceived acceptability of implementing MAS. Semi-structured interviews and a questionnaire were employed across participants categorized into four groups. It was found that government and industry participants held positive perceptions towards MAS, supporting its use and continued research in BC, and identifying its benefits in forest regeneration and to tree breeders. Environmental non-governmental organizations (ENGOs) and First Nations attitudes lay between neutral and negative. Concerns were most strongly focused on environmental impacts, ecosystem degradation, and reduced genetic diversity, while identified benefits were specific to tree breeders and improved tree resiliency. It was concluded that before MAS can be successfully implemented, an appropriate setting must first be established through improved knowledge of biotechnology and its applications, well-defined policies, and strengthened engagement and consultation with First Nations.
Reviewing hybrid coronary revascularization: challenges, controversies and opportunities

ABSTRACT Two main approaches to myocardial revascularization currently exist, coronary artery bypass and percutaneous coronary intervention. In patients with advanced coronary artery disease, coronary artery bypass surgery is associated with improved long term outcomes while percutaneous coronary intervention is associated with lower periprocedural complications. A new approach has emerged in the last decade that attempts to reap the benefits of bypass surgery and stenting while minimizing the shortcomings of each approach. This new approach, hybrid coronary revascularization, has shown encouraging early results. Minimally invasive techniques for bypass surgery have played a large part of bringing this approach into contemporary practice.
Restriction site‐associated DNA sequencing generates high‐quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China

Bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are invasive species and listed as US federally injurious species under the Lacy Act. They have established populations in much of the Mississippi River Basin (MRB; Mississippi, Illinois, and Missouri rivers) and are capable of producing fertile hybrids and complex introgression. Characterizing the composition of this admixture requires a large set of high‐quality, evolutionarily conserved, diagnostic genetic markers to aid in the identification and management of these species in the midst of morphological ambiguity. Restriction site‐associated DNA (RAD) sequencing of 45 barcoded bighead and silver carp from the United States and China produced reads that were aligned to the silver carp transcriptome yielded 261 candidate single nucleotide polymorphisms (SNPs) with fixed allelic differences between the two species. We selected the highest quality 112 SNP loci for validation using 194 putative pure‐species and F1 hybrids from the MRB and putative bighead carp and silver carp pure species from China (Amur, Pearl and Yangtze rivers). Fifty SNPs were omitted due to design/amplification failure or lack of diagnostic utility. A total of 57 species‐diagnostic SNPs conserved between carp species in US and Chinese rivers were identified; 32 were annotated to functional gene loci. Twenty‐seven of the 181 (15%) putative pure species were identified as hybrid backcrosses after validation, including three backcrosses from the Amur River, where hybridization has not been documented previously. The 57 SNPs identified through RAD sequencing provide a diagnostic tool to detect population admixture and to identify hybrid and pure‐species Asian carps in the United States and China.
Random genetic drift, natural selection, and noise in human cranial evolution.

OBJECTIVES This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. MATERIALS AND METHODS Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. RESULTS Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. DISCUSSION The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc.
Face alignment by minimizing the closest classification distance

In this paper, we present a face registration approach, in which alignment is done by minimizing the closest distance at the classification step. This method eliminates the need of a feature localization step that exists in traditional face recognition systems and formulates alignment as an optimization process during classification. In other words, instead of performing a separate facial feature localization step and localizing facial features according to some type of feature matching score, in the proposed method, alignment is done by directly optimizing the classification score. Moreover, a feature detector can still be integrated to the system. In this case, the output of the feature detector is used as the initial point of the optimization process. Results of extensive experiments have shown that the proposed approach leads very high correct recognition rates, especially in the case of partial face occlusion, where it is not possible to precisely detect the facial feature locations. It has been also found that, in the case of using a facial feature detector, the approach can tolerate localization errors of up to 18% of the interocular distance.
Single-port video-assisted thoracic surgery in 1063 cases: a single-institution experience†.

OBJECTIVES Single-port video-assisted thoracic surgery (VATS) technique has been used for thoracic diseases. There was no report about single-port VATS in large series. Outcomes following single-port VATS were analysed to determine its efficacy and safety. METHODS From June 2012 to June 2014, 1063 single-port VATSs were performed by four surgeons. Patient demographics, perioperative parameters, histopathology and outcomes were analysed. RESULTS There were 1063 patients (524 men and 539 women). The median age was 56.1 ± 8.7 years (range, 15-86 years). Lobectomy was performed in 569 patients, segmentectomy in 162, wedge resection in 264, pleural biopsy in 7, drainage of effusion in 20, pleural tumour resection in 5, mediastinal tumour resection in 54, mediastinal tumour biopsy in 2, bilobectomy in 7, sleeve lobectomy in 3 and pneumonectomy in 2. Synchronous bilateral single-port VATS was performed in 27 cases, whereas metachronous bilateral single-port VATS was performed in 5 cases. Pathological diagnoses included primary lung cancer in 635 cases, metastatic lung cancer in 19, mediastinal tumour in 56, pleural disease in 32 and benign pulmonary conditions in 353. Fifteen intraoperative vascular injuries were identified in 15 patients. The total conversion rate was 4.6%. The average operation time was 135 ± 31 min (range, 30-230 min), and the average blood loss was 117 ± 47 ml (range, 50-2000 ml). The median intensive care unit stay was 1 day (0-4 days). The postoperative hospital stay was 6.2 ± 2.6 days on average. There was no operative death, and operative complications occurred in 59 patients (5.6%). The 1-year overall survival and 1-year disease-free survival for the primary lung cancer group were 98 and 96%, respectively. CONCLUSIONS Our findings indicate that single-port VATS for thoracic diseases is safe and feasible.
Bacterial meningitis in the elderly.

To the Editor. —Because individuals older than 65 years now comprise 20% of our country's population of which the over 80 age group is the fastest growing segment, the article by Gorse et al 1 is both pertinent and topical. As with other geriatric infections we need to determine whether incidence is increasing or whether the population shift accounts for the rising number of cases. Etiologies and the setting in which the disease occurs will need to be documented carefully if, as in other age groups, we are to select appropriate therapy while microbiologic studies are pending. It is anticipated that early therapy will continue to be mandatory for a condition in which delays lead to an unacceptable morbidity and mortality and are untenable. The study by Gorse et al is retrospective and suffers from problems inherent in all such endeavors. However, it seems clear from their morbidity and mortality
C O ] 7 F eb 2 00 7 ON QUARTIC HALF-ARC-TRANSITIVE METACIRCULANTS

Following Alspach and Parsons, a metacirculant graph is a graph admitting a transitive group generated by two automorphisms ρ and σ, where ρ is (m,n)semiregular for some integers m ≥ 1, n ≥ 2, and where σ normalizes ρ, cyclically permuting the orbits of ρ in such a way that σ has at least one fixed vertex. A half-arc-transitive graph is a vertexand edgebut not arc-transitive graph. In this article quartic half-arc-transitive metacirculants are explored and their connection to the so called tightly attached quartic half-arc-transitive graphs is explored. It is shown that there are three essentially different possibilities for a quartic halfarc-transitive metacirculant which is not tightly attached to exist. These graphs are extensively studied and some infinite families of such graphs are constructed.
The yeast orthologue of GRASP 65 forms a complex with a coiled-coil protein that contributes to ER to Golgi traffi c

Formation of the fi rst compartment of the Golgi apparatus involves recognition events between several different membranes. These include tethering of both anterograde COPII vesicles and retrograde COPI vesicles to the cis-Golgi. In addition, intermediate compartment structures that formed in the cell periphery fuse with the cis-Golgi membranes after movement to the cell center, and Golgi stacks undergo homotypic fusion to form the elongated ribbon characteristic of vertebrate cells. Finally, the cis-Golgi is attached to an adjacent medial compartment in the stack. Several proteins have been proposed to guide these membrane recognition events, including the coiled-coil proteins GM130 and p115, the multisubunit complexes transport protein particle (TRAPP) and conserved oligomeric Golgi (COG), and the PDZ-like protein GRASP65 (Whyte and Munro, 2002; Barr and Short, 2003). This latter protein was identifi ed using an in vitro assay for the postmitotic reassembly of mammalian Golgi stacks (Barr et al., 1997). It consists of two PDZ-like domains fl anked by a C-terminal Ser/ Pro-rich domain and an N-terminal myristoylation site, which is required for its association with the cis-Golgi (Barr et al., 1998; Kondylis et al., 2005). GRASP65 recruits the coiled-coil protein GM130 to the cis-Golgi by binding to the latter’s C terminus (Barr et al., 1997). Golgi association of the two proteins appears mutually interdependent, as mutation of the interfacial residues in either protein causes a loss of localization (Barr et al., 1998). GRASP55, a GRASP65 paralogue unique to vertebrates, is found on the medial Golgi but may also contribute to GM130 recruitment (Shorter et al., 1999; Vasile et al., 2003). GM130 also interacts with the coiled-coil protein p115 and the small GTPase Rab1, and it has been proposed that the GRASP65– GM130 complex acts in a variety of tethering interactions at the cis-Golgi (Nakamura et al., 1997; Weide et al., 2001; Kondylis et al., 2005; Puthenveedu et al., 2006). Despite these compelling physical interactions, analysis of the importance of GRASP65 in vivo has not yet reached a clear consensus. Removal of the protein by RNAi has been reported to affect the formation of Golgi ribbons, the number of cisternae, the structure of the cisternae themselves, and even the formation of the mitotic spindle (Kondylis et al., 2005; Sutterlin et al., 2005; Puthenveedu et al., 2006). However, in all cases, transport through the Golgi appeared relatively normal, and a similar result has been reported for the loss of GM130 (Vasile et al., 2003). These rather variable and perhaps surprisingly mild phenotypes may refl ect a degree of redundancy in membrane traffi c steps at the cis-Golgi. Not only are there other large The yeast orthologue of GRASP65 forms a complex with a coiled-coil protein that contributes to ER to Golgi traffi c
An abundance of heterotic vacua

We explicitly construct the largest dataset to date of heterotic vacua arising from stable vector bundles on Calabi-Yau threefolds. Focusing on elliptically fibered Calabi-Yau manifolds with spectral cover bundles, we show that the number of heterotic models with non-zero number of generations is finite. We classify these models according to the complex base of their Calabi-Yau threefold and to the unification gauge group that they preserve in four dimensions. This database of the order of 10^7 models, which includes potential Standard Model candidates, is subjected to some preliminary statistical analyses. The additional constraint that there should be three net generations of particles gives a dramatic reduction of the number of vacua.
Molecular dynamics simulations on the effects of moisture on the interfacial adhesion properties of glass fibre-epoxy composites

xi Nomenclature . xiv
Designer Collagen-Fibril Biograft Materials for Tunable Molecular Delivery

Author: Joshi, Rucha, Vinay. Ph.D. Institution: Purdue University Degree Received: December 2016 Title: Designer Collagen-Fibril Biograft Materials for Tunable Molecular Delivery Major Professor: Sherry L. Voytik-Harbin One of the biggest challenges in tissue engineering currently is the formation of a functional microvascular network as part of an engineered tissue graft. Despite many advances in tissue engineering methods, the field still awaits biograft designs that enable neovascularization at clinically relevant size scales. Critical to the design of such materials are tissue-specific physico-mechanical properties and controlled local therapeutic molecular release. The purpose of the current research is to develop such a multifunctional biograft material from type I collagen polymers. Although collagen-based biomaterials have been applied broadly to tissue engineering and local drug delivery applications, persistent shortcomings remain, including poor mechanical properties, rapid proteolytic degradation, and cursory control over physical properties and molecular release profiles. In large part, this is owing to 1) poor characterization of conventional formulations in terms of their molecular composition and 2) inability to fully capitalize on the inherent self-assembly or polymerization capacity of collagen. Here we address current shortcomings through the development of self-assembling, collagen-fibril biograft materials through integrated tissue engineering and molecular delivery design. More specifically, collagen polymers specified by their intermolecular crosslink composition and self-assembly capacity were used to customize and design materials in terms of 1) collagen fibril microstructure and 2) proteolytic degradability, collectively defining overall local molecular release profiles. Application of the designed collagen biograft materials to control vascular endothelial growth factor (VEGF) release for promoting neovascularization and tissue regeneration was shown using an established in-vivo chicken egg chorioallantoic membrane (CAM) model.