Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence of the Sugar Pine Megagenome

Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly repetitive, 31 billion bp genome. It is the largest genome sequenced and assembled to date, and the first from the subgenus Strobus, or white pines, a group that is notable for having the largest genomes among the pines. The genome represents a unique opportunity to investigate genome “obesity” in conifers and white pines. Comparative analysis of P. lambertiana and P. taeda L. reveals new insights on the conservation, age, and diversity of the highly abundant transposable elements, the primary factor determining genome size. Like most North American white pines, the principal pathogen of P. lambertiana is white pine blister rust (Cronartium ribicola J.C. Fischer ex Raben.). Identification of candidate genes for resistance to this pathogen is of great ecological importance. The genome sequence afforded us the opportunity to make substantial progress on locating the major dominant gene for simple resistance hypersensitive response, Cr1. We describe new markers and gene annotation that are both tightly linked to Cr1 in a mapping population, and associated with Cr1 in unrelated sugar pine individuals sampled throughout the species’ range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of the Cr1 region are resources for future marker-assisted breeding efforts as well as for investigations of fundamental mechanisms of invasive disease and evolutionary response.
Dendritic cells in the T‐cell areas of lymphoid organs

Summary: Substantial numbers of dendritic cells (DCs) are found in the T‐cell areas of peripheral lymphoid organs such as the spleen, lymph node and Peyer's patch. By electron microscopy these DCs (also called interdigitating cells) form a network through which T cells continually recirculate. The cytological features of DCs in the T‐cell areas, as well as a number of markers detected with monoclonal antibodies, are similar to mature DCs that develop from other sites such as skin and bone marrow. Some markers that are expressed in abundance are: MHC II and the associated invariant chain, accessory molecules such as CD40 and CD86, a multilectin receptor for antigen presentation called DEC‐205, the integrin CD11c, several antigens within the endocytic system that are detected by monoclonal anti‐bodies but are as yet uncharacterized at the molecular level, and, in the human system, molecules termed Sl00b, CD83 and p55. DCs in the periphery can pick up antigens and migrate to the T‐cell areas to initiate immunity However, there are new observations that DCs within the T‐cell areas also express high levels of self‐antigens and functional fas‐ligand capable of Inducing CD4+ T‐cell death. We speculate that there are at least 2 sets of DCs in the T‐cell areas, a migratory myeloid pathway that brings in antigens from the periphery and induces immunity, and a more resident lymphoid pathway that presents self‐antigens and maintains tolerance.
Green Light Stimulates Early Stem Elongation, Antagonizing Light-Mediated Growth Inhibition1

During the transition from darkness to light, the rate of hypocotyl elongation is determined from the integration of light signals sensed through the phototropin, cryptochrome, and phytochrome signaling pathways. In all light conditions studied, from UV to far-red, early hypocotyl growth is rapidly and robustly suppressed within minutes of illumination in a manner dependent upon light quality and quantity. In this study, it is shown that green light (GL) irradiation leads to a rapid increase in the growth rate of etiolated Arabidopsis seedlings. GL-mediated growth promotion was detected in response to constant irradiation or a short, single pulse of light with a similar time course. The response has a threshold between 10−1 and 100 μmol m−2, is saturated before 102 μmol m−2 and obeys reciprocity. Genetic analyses indicate that the cryptochrome or phototropin photoreceptors do not participate in the response. The major phytochrome receptors influence the normal amplitude and timing of the GL response, yet the GL response is normal in seedlings grown for hours under constant dim-red light. Therefore, phytochrome activation enhances, but is not required for, the GL response. Seedlings grown under green, red, and blue light together are longer than those grown under red and blue alone. These data indicate that a novel GL-activated light sensor promotes early stem elongation that antagonizes growth inhibition.
Immunocytochemical localization of DARPP‐32, a dopamine and cyclic‐ AMP‐regulated phosphoprotein, in the primate brain

The localization of DARPP‐32, a dopamine and cAMP‐regulated phosphoprotein, has been studied in monkey brain by immunocytochemistry. This study indicates that DARPP‐32 is enriched in neurons in regions receiving a dense dopamine input from the substantia nigra and ventral tegmental area. Thus, the majority of somata in the anterior olfactory area, nucleus accumbens, caudate nucleus, and putamen are immunoreactive for DARPP‐32. In the caudate nucleus, immunoreactive spines receive asymmetric contacts from unlabeled axon terminals. Immunoreactive somata have diameters of 10–15 μm. In regions known to receive projections from these nuclei, immunoreactivity is confined to small puncta that represent axons and axon terminals. Regions in which immunoreactivity is present in puncta include the ventral pallidum, globus pallidus, and substantia nigra pars reticulata. Dopaminergic neurons themselves are not immunoreactive.
Protein crystals for the delivery of biopharmaceuticals

The year 2002 marked the 20th anniversary of the first successful product of modern biotechnology, the regulatory approval of recombinant insulin for biopharmaceutical applications. Insulin is also the first crystalline protein to be approved for therapeutic use. Over the past two decades, almost 150 biopharmaceuticals have gained marketing authorisation; however, insulin remains the only crystalline protein on the market. Significant research and development efforts have focused on the engineering of protein molecules, efficacy testing, model development, and protein production and characterisation. These advances have dramatically boosted the therapeutic applications of proteins, which now include treatments against acute conditions, such as cancer, cardiovascular disease and viral disease, and chronic conditions, such as diabetes, growth hormone deficiency, haemophilia, arthritis, psoriasis and Crohn’s disease. Despite these successes, many challenges normally associated with biopharmaceuticals, such as poor stability and limited delivery options, remain. Protein crystals have shown significant benefits in the delivery of biopharmaceuticals to achieve high concentration, low viscosity formulation and controlled release protein delivery. This review will discuss challenges related to the broader utilisation of protein crystals in biopharmaceutical applications, as well as recent advances and valuable new directions that protein crystallisation-based technologies present.
Comparative analysis of Lean and Six Sigma improvement projects: performance, changes, investment, time and complexity

This paper describes a study of the effectiveness of Lean and Six-Sigma improvement projects. The purpose of this study is to analyse and compare improvement projects in Lean and Six-Sigma contexts based on two groups of variables – resources and results of projects. The variables related to the resources are financial investment, time, complexity of the team, complexity of the method, complexity of the tools and techniques and complexity of the training. The variables related to the results are performance impact and level of change. We developed a multiple case study on 18 Lean and Six-Sigma projects. We found a positive association between the variables of team complexity and level of change, as well as between the variables of training and complexity of the method, tools and techniques. These results highlight the importance of resource decisions for improvement projects, especially the team’s composition and level of training. The comparison between Lean and Six-Sigma projects showed that no significant differences were identified in the variables of the results (performance impact and change level). There were differences in time, complexity of tools and techniques and complexity of training. Practically, the analysis allows for more effective resource management in Six-Sigma and Lean projects.
Optimal infectivity in vitro of human immunodeficiency virus type 1 requires an intact nef gene

The replication competence of human immunodeficiency virus type 1 genomes containing mutations in the nef open reading frame was evaluated in continuous cell lines. Mutants that contained a deletion in the nef open reading frame, premature termination codons, or missense mutations in the N-terminal myristoylation signal were constructed. The replication of these mutants was tested in three ways. First, plasmid genomes were used to transfect T-lymphoblastoid cells. Second, low-passage posttransfection supernatants were used to infect cells with a relatively low virus input. Third, high-titer virus stocks were used to infect cells with a relatively high virus input. These experiments demonstrated a 100- to 10,000-fold decrement in p24 production by the nef mutants compared with that by the wild-type virus. The greatest difference was obtained after infection with the lowest virus input. The myristoylation signal was critical for this positive effect of nef. To investigate the mechanism of the positive influence of nef, nef-positive and nef-minus viruses were compared during a single cycle of replication. These single-cycle experiments were initiated both by infection with high-titer virus stocks and by transfection with viral DNA. Single-cycle infection yielded a three- to fivefold decrement in p24 production by nef-minus virus. Single-cycle transfection yielded equal amounts of p24 production. These results implied that nef does not affect replication after the provirus is established. In support of these results, viral production from cells chronically infected with nef-positive or nef-minus viruses was similar over time. To determine whether the effect of nef was due to infectivity, end point titrations of nef-positive and nef-minus viruses were performed. nef-positive virus had a greater infectivity per picogram of HIV p24 antigen than nef-minus virus. These data indicated that the positive influence of nef on viral growth rate is due to an infectivity advantage of virus produced with an intact nef gene.
Translational recruitment of Xenopus maternal mRNAs in response to poly(A) elongation requires initiation factor eIF4G-1.

Xenopus oocytes accumulate maternal mRNAs which are then recruited to ribosomes during meiotic cell cycle progression in response to progesterone and coincident with poly(A) elongation. Prior to stimulation, most protein synthesis ( approximately 70%) does not require intact translation factor eIF4G (B. D. Keiper and R. E. Rhoads, 1997, Nucleic Acids Res. 25, 395-402). In the present study we have addressed the requirement of eIF4G in the recruitment of mRNAs during meiosis. Cleavage of eIF4G by coxsackievirus protease 2A inhibited progesterone-induced meiotic progression in 88% of the oocytes; prevented the recruitment of maternal mRNAs encoding cyclin B1, c-Mos, D7, and B9; and disrupted the association of eIF4G with poly(A)-binding protein. Poly(A) elongation, however, was not inhibited by eIF4G cleavage. Injection of MPF restored meiotic cell cycle progression to >60% of the oocytes but not the recruitment of cyclin B1 or B9 mRNA. Previously recruited maternal mRNAs were removed from polyribosomes following subsequent cleavage of eIF4G, indicating that eIF4G is required both to recruit and also to maintain maternal mRNAs on polyribosomes. The expression of a cleavage-resistant variant of human eIF4G-1 (G486E) significantly restored the ability to synthesize c-Mos in response to progesterone and to translate exogenous beta-globin mRNA, indicating that the inhibition by protease 2A is due to cleavage of eIF4G alone. These results indicate that intact eIF4G is required for the poly(A)-dependent recruitment of several maternal mRNAs (cyclin B1, c-Mos, D7, and B9) during meiotic cell cycle progression but not for the synthesis of most proteins.
Regression-based estimates of observed functional status in centenarians.

PURPOSE OF THE STUDY There is lack of consensus on the best method of functional assessment, and there is a paucity of studies on daily functioning in centenarians. We sought to compare associations between performance-based, self-report, and proxy report of functional status in centenarians. We expected the strongest relationships between proxy reports and observed performance of basic activities of daily living (BADLs) and instrumental activities of daily living (IADLs). We hypothesized that the discrepancy between self-report and observed daily functioning would be modified by cognitive status. We additionally sought to provide clinicians with estimates of centenarians' observed daily functioning based on their mental status in combination with subjective measures of activities of daily living (ADLs). DESIGN AND METHODS Two hundred and forty-four centenarians from the Georgia Centenarian Study were included in this cross-sectional population-based study. Measures included the Direct Assessment of Functional Status, self-report and proxy report of functional status, and the Mini-Mental State Examination (MMSE). RESULTS Associations between observed and proxy reports were stronger than between observed and self-report across BADL and IADL measures. A significant MMSE by type of report interaction was found, indicating that lower MMSE performance is associated with a greater discrepancy between subjective and objective ADL measures. IMPLICATIONS Results demonstrate associations between 3 methods of assessing functional status and suggest proxy reports are generally more accurate than self-report measures. Cognitive status accounted for some of the discrepancy between observed and self-reports, and we provide clinicians with tables to estimate centenarians' performance on observed functional measures based on MMSE and subjective report of functional status.
Falls and fear of falling in vertigo and balance disorders: A controlled cross-sectional study.

BACKGROUND Vertigo and dizziness are among the most prevalent symptoms in neurologic disorders. Although many of these patients suffer from postural instability and gait disturbances, there is only limited data on their risk of falling. METHODS We conducted a controlled cross-sectional study at the tertiary care outpatient clinic of the German Center for Vertigo and Balance Disorders using a self-administered questionnaire to assess falls, fall-related injuries, and fear of falling. The recruitment period was 6 months. RESULTS A total of 569 patients (mean age 59.6 ± 17.1 years, 55% females) and 100 healthy participants were included (response rate > 90%). Dizzy patients with central balance disorders (Parkinsonian, cerebellar, and brainstem oculomotor syndromes) had the highest fall rates (> 50% recurrent fallers, odds ratio > 10). The rate of recurrent fallers was 30% in bilateral vestibular failure and peripheral neuropathy (odds ratio > 5). Patients with functional dizziness (somatoform or phobic vertigo) were concerned about falling but did not fall more often than healthy controls (odds ratio 0.87). CONCLUSION Falls are common in patients presenting to a dizziness unit. Those with central syndromes are at risk of recurrent and injurious falling. Fall rates and fear of falling should be assessed in balance disorders and used to guide the regimen of rehabilitation therapy. The identification of risk factors would help provide protective measures to these groups of patients.
Successful pregnancy with frozen embryo transfer into a gestational carrier from eggs obtained from a woman in premature menopause.

PURPOSE To describe a unique case of a successful gestational carrier pregnancy in a woman with premature ovarian failure using her own oocyte. METHODS Despite amenorrhea, failure to have menses to progesterone withdrawal and resistance to gonadotropin stimulation, ovulation induction was attempted by restoring down-regulated follicle stimulating hormone (FSH) receptors by lowering the elevated serum FSH and allowing stimulation by endogenous or exogenous gonadotropins. Oocyte retrieval was attempted if a mature follicle was obtained. GnRH antagonist was used to prevent premature oocyte release. Tapering prednisone was used for the first five days of the cycle due to patient's history of autoimmune disease (vasculitis and Crohn's disease). IVIG was given 8/2003 for vasculitis. RESULTS The patient underwent a total of 19 attempted retrievals during continuous natural cycles from 3/2003 to 2/2007. Oocyte retrieval required traversing the uterus with the retrieval needle because of ovarian position after multiple surgeries for bilateral endometriomas and Crohn's disease. Empty follicle syndrome was encountered in four retrieval attempts. In 15 attempts, an oocyte was obtained. The sole attempt at natural fertilization failed. ICSI and assisted hatching were used in all subsequent attempts, and were successful in all but one attempt which led to a 3 pronuclei embryo which was discarded. The first four single embryos retrieved (7, 4, 6 cells and morula) were all A1 or A2 and transferred fresh to the patient, but no pregnancy resulted. All subsequent embryos were cryopreserved. The transfer of four embryos (6-cell and 7-cell and 3-cell and 8-cell) in two cycles to two different gestational carriers resulted in a successful delivery of a full-term healthy female infant 3.3 kg. Genetic testing confirmed maternal identity to be the patient, not the carrier. CONCLUSIONS This is the first reported case of a successful gestational carrier pregnancy after reversing ovarian failure, inducing ovulation, and transferring a frozen-thawed embryo.
NF1 Gene Expression in Mouse Fracture Healing and in Experimental Rat Pseudarthrosis

Neurofibromatosis type 1 (NF1) is an inherited disease with an incidence of about 1:3000 worldwide. Approximately half of all patients with NF1 present osseous manifestations, which can vary from mild to severely debilitating changes such as congenital pseudarthrosis. In the present study, fracture healing of mouse tibia was followed and specimens were collected 5, 9, 14, and 22 days postoperatively. Experimental pseudarthrosis of rat was followed up to 15 weeks postoperatively. In situ hybridization and immunohistochemistry were used to demonstrate expression of NF1 tumor suppressor and phosphorylated p44/42 mitogen-activated protein kinase (MAPK), an indicator of the Ras-MAPK pathway. The results showed that ossified callus was formed in mouse fracture 22 days after the operation. The final outcome of rat pseudarthrosis was detected 9 weeks after the operation, presenting abundant cartilaginous callus at the pseudarthrosis. NF1 gene expression was noted in the maturing and in the hypertrophic cartilages during normal mouse fracture healing, and in rat pseudarthrosis. Phosphorylated p44/42 MAPK was detected in a subpopulation of the hypertrophic chondrocytes in both models. Furthermore, positive labeling for NF1 mRNA and protein was detected in endothelium in both the pseudarthrosis and in the fracture. In conclusion, NF1 gene expression and function are needed for normal fracture healing, possibly restraining excessive Ras-MAPK pathway activation.
Assessing Tool for the Professional Profile of the Candidate School Directors-The Greek Legislative Framework

In order to fill the positions of the executives of the public education, and in particular for the selection of Directors of Secondary General Education Schools, teachers of public Education are selected on the basis of tables that drawn up according to the provisions of the respective laws. The research aimed to analyze the issue of evaluation/assessment of the professional profile of the School Directors-Candidates in Secondary Education, with the synthesis of the assessing criteria used in the last 20 years in Greece by the Ministry of Education in order to create, as result, an assessing tool for the selection of school directors. Through the research it is attempted to highlight how professionally structured the Greek legislation requires to be the Directors of Secondary Education, i.e. how scientifically and pedagogically trained (I), how its administrative and downstream experience (II) is valued and how their Personality (III) are. The results of the research are pictured in the ‘Assessing Tool for the Candidate School Director's Professional Profile', in Secondary Education.
Amiloride‐sensitive channels are a major contributor to mechanotransduction in mammalian muscle spindles

We investigated whether channels of the epithelial sodium/amiloride‐sensitive degenerin (ENaC/DEG) family are a major contributor to mechanosensory transduction in primary mechanosensory afferents, using adult rat muscle spindles as a model system. Stretch‐evoked afferent discharge was reduced in a dose‐dependent manner by amiloride and three analogues – benzamil, 5‐(N‐ethyl‐N‐isopropyl) amiloride (EIPA) and hexamethyleneamiloride (HMA), reaching ≥85% inhibition at 1 mm. Moreover, firing was slightly but significantly increased by ENaC δ subunit agonists (icilin and capsazepine). HMA's profile of effects was distinct from that of the other drugs. Amiloride, benzamil and EIPA significantly decreased firing (P < 0.01 each) at 1 μm, while 10 μm HMA was required for highly significant inhibition (P < 0.0001). Conversely, amiloride, benzamil and EIPA rarely blocked firing entirely at 1 mm, whereas 1 mm HMA blocked 12 of 16 preparations. This pharmacology suggests low‐affinity ENaCs are the important spindle mechanotransducer. In agreement with this, immunoreactivity to ENaC α, β and γ subunits was detected both by Western blot and immunocytochemistry. Immunofluorescence intensity ratios for ENaC α, β or γ relative to the vesicle marker synaptophysin in the same spindle all significantly exceeded controls (P < 0.001). Ratios for the related brain sodium channel ASIC2 (BNaC1α) were also highly significantly greater (P < 0.005). Analysis of confocal images showed strong colocalisation within the terminal of ENaC/ASIC2 subunits and synaptophysin. This study implicates ENaC and ASIC2 in mammalian mechanotransduction. Moreover, within the terminals they colocalise with synaptophysin, a marker for the synaptic‐like vesicles which regulate afferent excitability in these mechanosensitive endings.
Fast four‐dimensional coronary MR angiography with k‐t GRAPPA

To investigate the effectiveness of k‐t GRAPPA for accelerating four‐dimensional (4D) coronary MRA in comparison with GRAPPA and the feasibility of combining variable density undersampling with conventional k‐t GRAPPA (k‐t2 GRAPPA) to alleviate the overhead of acquiring autocalibration signals.