Miracle-dz/UniFAR-FTUs huggingface dataset:
Helicobacter pylori determinants of pathogenicity.

The bacterium Helicobacter pylori colonises the stomach of man and induces a strong inflammatory response. Differences in the possession of pathogenicity determinants by H. pylori isolates could account in part for the different clinical outcomes of infection. The main H. pylori pathogenic factors, i.e. urease, the cytotoxin VacA, and the genes involved in virulence contained in the pathogenicity island (PAI) cag, may promote tissue damage and ulceration, and could contribute to gastric cancer development. Strains with the mosaic vacA allelic type s1a/m1 and possessing the cag insertion are considered endowed with increased inflammatory potential, and are more likely to be isolated from patients with peptic ulcer and gastric cancer. The presence in H. pylori cag PAI of operons involved in the stimulation of gastric epithelial cells to secrete high levels of inflammatory cytokines, in mobilisation of DNA, and formation of secretory mechanisms and conjugation apparati, could contribute to increase the risk of gastric cancer development in patients infected by this microorganism.
RNA Polymerase II C-Terminal Domain Phosphorylation Patterns in Caenorhabditis elegans Operons, Polycistronic Gene Clusters with Only One Promoter

ABSTRACT The heptad repeat of the RNA polymerase II (RNAPII) C-terminal domain is phosphorylated at serine 5 near gene 5′ ends and serine 2 near 3′ ends in order to recruit pre-mRNA processing factors. Ser-5(P) is associated with gene 5′ ends to recruit capping enzymes, whereas Ser-2(P) is associated with gene 3′ ends to recruit cleavage and polyadenylation factors. In the gene clusters called operons in Caenorhabditis elegans, there is generally only a single promoter, but each gene in the operon forms a 3′ end by the usual mechanism. Although downstream operon genes have 5′ ends, they receive their caps by trans splicing rather than by capping enzymes. Thus, they are predicted to not need Ser-5 phosphorylation. Here we show by RNAPII chromatin immunoprecipitation (ChIP) that internal operon gene 5′ ends do indeed lack Ser-5(P) peaks. In contrast, Ser-2(P) peaks occur at each mRNA 3′ end, where the 3′-end formation machinery binds. These results provide additional support for the idea that the serine phosphorylation of the C-terminal domain (CTD) serves to bring RNA-processing enzymes to the transcription complex. Furthermore, these results provide a novel demonstration that genes in operons are cotranscribed from a single upstream promoter.
Nested Invariant 3-Tori Embedded in a Sea of Chaos in a quasiperiodic Fluid Flow

Nested invariant 3-tori surrounding a torus braid of elliptic type are found to exist in a model of a fluid flow with quasiperiodic forcing. The Hamiltonian describing the system is given by the superposition of two steady stream functions, one with an elliptic fixed point and the other with a coincident hyperbolic fixed point. The superposition, modulated by two incommensurate frequencies, yields an elliptic torus braid at the location of the fixed point. The system is suspended in a four-dimensional phase space (two space and two phase directions). To analyze this system we define two three-dimensional, global, Poincare sections of the flow. The coherent structures (cross-sections of nested 2 tori) are found each to have a fractal dimensional of two, in each Poincare cross-section. This framework has applications to tidal and other mixing problems of geophysical interest.
An Ashkenazi Jewish woman presenting with favism

The case of a 44 year old Ashkenazi Jewish woman of Russian origin who presented with a typical clinical and haematological picture of favism is reported. There was initial difficulty in confirming glucose-6-phosphate dehydrogenase (G6PD) deficiency because the enzyme concentrations were normal at presentation, but later fell to a concentration compatible with heterozygosity for the Mediterranean type of G6PD deficiency. The diagnosis was also later confirmed by gene analysis. The reasons for the difficulties in the initial confirmation of the diagnosis and the normal G6PD enzyme activity at presentation are discussed.
Polarization-induced renormalization of molecular levels at metallic and semiconducting surfaces

On the basis of first-principles G0W0 calculations we systematically study how the electronic levels of a benzene molecule are renormalized by substrate polarization when physisorbed on different metallic and semiconducting surfaces. The polarization-induced reduction in the energy gap between occupied and unoccupied molecular levels is found to scale with the substrate density of states at the Fermi level for metals and substrate band gap for semiconductors. These conclusions are further supported by self-consistent GW calculations on simple lattice models. By expressing the electron self-energy in terms of the substrate’s joint density of states we relate the level shift to the surface electronic structure, thus providing a microscopic explanation of the trends in the GW and G0W0 calculations. While image charge effects are not captured by semilocal and hybrid exchange-correlation functionals, we find that error cancellations lead to remarkably good agreement between the G0W0 and Kohn-Sham energies for the occupied orbitals of the adsorbed molecule.
Fault tolerant control based on parametric estimation applied to diesel engine

In this paper, a fault tolerant control method based on the parametric estimation is presented and applied to the air path system of a diesel engine. This method uses directly the results of a parametric estimation of the system which is nonlinear and whose state variables and parameters are strongly coupled. Our goal is to adapt an Unconstrained Nonlinear Continuous-time Generalized Predictive Control (NCGPC) after detecting clearly, through a parametric variation, a fault occurred on a nonlinear model of Turbocharged Diesel Engine (TDE) published in the literature. Likewise, we will build a control strategy called Fault Tolerant Control (FTC) with which all detected dysfunctions and parametric variations will be taken into account.
CIRCADIAN RHYTHMS OF PLASMA CORTICOID LEVELS, INTRAOCULAR PRESSURE AND AQUEOUS OUTFLOW FACILITY IN NORMAL AND GLAUCOMATOUS EYES *

The mean intra-ocular pressure ( IOP) for normal eyes is 15 mm.Hg. and this pressure is'the result of a balanced inflow and outflow of aqueous humor. Aqueous inflow is the result of a secretion from the ciliary body. The flow passes between the lens and the iris, through the pupil into the anterior chamber, and then it is removed from the eye through a trabecular network in the angle, and so into the canal of Schlemm. Exit channels from the canal carry the aqueous humor into the episcleral venules on the outside of the eyeball a little posterior to the corneal margin. The control of inflow and outflow is not perfect, and there are variations in pressure, partly haphazard, but largely with a regular circadian rhythm. The pressure tends to be at its lowest in the late evening and early morning. Later in the morning it rises, reaching its maximum, usually between 8:OO A.M. and noon. If IOP has a circadian rhythm, then one must assume that there is also a circadian rhythm of aqueous inflow and aqueous outflow.
The Malarial Fevers of Jerusalem and their prevention

In a previous paper I referred to observations by Dr E. W. G. Masterman, on the prevalence of malaria in Jerusalem. Since that time Dr Masterman has searched various places for Anopheles in and near the city, and has found numerous larvae in the Birket Mamilla (or “Upper Pool of Gihon”) in winter, the water of which is conducted by covered conduits to Turkish baths in the city. The pool is dry in summer.
QuantiFERON-TB Gold Assay on Plasma for Confirmation of Presumed Tuberculosis-Related Uveitis

ABSTRACT The QuantiFERON-TB Gold assay was used to measure interferon gamma levels in plasma from 4 patients with presumed tuberculosis-related uveitis before, during, and after antitubercular therapy. After treatment, all patients showed clinical improvement. The concentrations showed a reversion to an absence of interferon gamma in one case, decreased in two cases, and remained stable in one case. These results suggest that the QuantiFERON assay may be useful for tuberculosis-related uveitis diagnosis and follow-up.
Neurally induced umbilical cord blood cells modestly repair injured spinal cords

Umbilical cord blood (UCB) is known to have stem/progenitor cells. We earlier showed that novel progenitors could be isolated from cryopreserved human UCB with high efficiency. The multipotent progenitor cells were induced to differentiate into neural-lineage cells under the appropriate condition. In this study, we confirmed these neurally induced progenitor cells (NPCs), containing higher quantities of nerve growth factor, promoted functional recovery in rats with spinal cord injury (SCI). Sprague–Dawley rats with SCI achieved a modest improvement in locomotor rating scale until 10 weeks after transplantation of the NPCs. SCI rats treated with NPCs also showed somatosensory-evoked potentials were recovered, and grafted cells especially exhibited oligodendrocytic phenotype around the necrotic cavity. These findings suggest that UCB-NPCs might be a therapeutic resource to repair damaged spinal cords.
Reduced bovine pancreatic trypsin inhibitor has a compact structure.

The conformation of reduced bovine pancreatic trypsin inhibitor (R-BPTI) under reducing conditions was monitored by measurements of nonradiative excitation energy-transfer efficiencies (E) between a donor probe attached to the N-terminal Arg1 residue and an acceptor attached to one of the lysine residues (15, 26, 41, or 46) [Amir, D. , & Haas, E. (1987) Biochemistry 26, 2162-2175]. High-excitation energy-transfer efficiencies that approach those found in the native state were obtained for the reduced labeled BPTI derivatives in 0.5 M guanidine hydrochloride (Gdn.HCl) and 4 mM DTT. Unlike the dependence expected for a random coil chain, E does not decrease as a function of the number of residues between the labeled sites. The efficiency of energy transfer between probes attached to residues 1 and 15 in the reduced state is higher than that found for the same pair of sites in the native state or reduced unfolded (in 6 M Gdn.HCl) state. This segment also shows high dynamic flexibility. These results indicate that the overall structure of reduced BPTI under folding (but still reducing) conditions shows a high population of conformers with interprobe distances similar to those of the native state. Reduced BPTI seems to be in a molten globule state characterized by a flexible, compact structure, which probably reorganizes into the native structure when the folding is allowed to proceed under oxidizing conditions.
Vitamin E-modified filters modulate Jun N-terminal kinase activation in peripheral blood mononuclear cells.

BACKGROUND The generation during hemodialysis of activated complement fragments and reactive oxygen species, including nitric oxide (NO), may affect peripheral blood mononuclear cell (PBMC) function. Currently, little is known about signal transduction pathways involved in PBMC activation. Jun N-terminal kinase (JNK) is a novel mitogen-activated protein (MAP) kinase phosphorylated and activated in response to oxidative stress and directly involved in cell activation. METHODS The present study evaluated the activation of JNK in PBMCs isolated from eight uremic patients undergoing, in a randomized manner, three month-subsequent periods of hemodialysis with a low-flux cellulose acetate (CA) and a vitamin E-modified cellulose membrane (CL-E). After each period of treatment, PBMCs were harvested before (T0), during (T15) and after three hours (T180) of dialysis. At the indicated time points, plasma C5b-9 generation by ELISA and inducible NO synthase (iNOS) gene expression by in situ hybridization were evaluated also. The activation of JNK was studied by Western blotting using a specific monoclonal anti-phospho-JNK antibody, which recognizes the activated form of JNK. RESULTS At T0, a significant increase in plasma C5b-9 levels was found in CA patients compared to CL-E-treated patients. During hemodialysis, C5b-9 levels rose more significantly in CA patients than in CL-E patients and returned to baseline values only in CL-E patients. At the same time, in CA patients an increased iNOS gene expression was observed at T180 together with a striking activation of JNK. By contrast, PBMC from CL-E-treated patients showed undetectable levels of phospho-JNK and a significant reduction in iNOS expression. Interestingly, incubation of PBMCs with normal human plasma (10%), activated by contact with a cellulosic membrane, induced a time-dependent increase in JNK phosphorylation that was completely inhibited by blocking complement cascade activation. CONCLUSION Our data suggest that JNK phosphorylation is strikingly increased in PBMCs obtained from CA-treated patients and may represent a key cellular event in PBMC activation during dialysis with bioincompatible membranes. The activation of this signaling enzyme, mediated by active complement fragments and PBMC-dialyzer interaction, can be significantly reduced by the use of vitamin E-coated membrane.
Decreasing Variation in the Use of Hospice Among Older Adults With Breast, Colorectal, Lung, and Prostate Cancer

BackgroundUtilization of hospice services has been shown to vary by place of residence and patient characteristics. Objectives.The purpose of this study was to examine whether such variation has changed over time. Hospice utilization is examined as a function of sociodemographic characteristics, geographic location, type of insurance, and year of death. Research DesignThis study used a retrospective cohort design. Subjects.We used data from the linked Surveillance, Epidemiology and End Results (SEER)–Medicare database to study hospice utilization in subjects aged 67 and older diagnosed with breast, colorectal, lung, or prostate cancer from 1991 to 1996 and who died between 1991 and 1999. ResultsOf the 170,136 subjects aged 67 and older who died from 1991 through 1999, 51,345 (30.2%) were enrolled in hospice before they died. Hospice utilization varied significantly by patient characteristics, including type of insurance, age, marital status, race and ethnicity, gender, urban versus rural residence, type of cancer, income level, and education level. This variation, however, decreased over time for subgroups defined by type of insurance, marital status, urban residence, and income. Variation in hospice use increased over time as a function of age and type of cancer. There was no change in variation in use in blacks compared with non-Hispanic whites over time. ConclusionsThe variation in hospice use by several patient characteristics is decreasing over time, a finding consistent with the manner in which new medical technologies diffuse.
Death after head injury: the 13 year outcome of a case control study

Background Head injury is common, and the risk of subsequent disability and death is high. Increased risk of death years after injury might be explained by factors associated with, but not a consequence of, the head injury. This unique prospective study investigates mortality over 13 years after injury. Methods A cohort of n=767 with head injury was compared with two case control groups, matched for age, gender and deprivation, and in one control group, matched for duration of hospital admission following (non-head) injury. Results Two-fifths of the head injury cohort had died. The death rate (30.99 per 1000 per year) was much higher than in community controls (13.72 per 1000 per year). More than 1 year after injury, the death rate in younger (15–54 years) adults was much higher than in community controls (17.36 vs 2.36 per 1000 per year) whereas in older adults the difference was more marginal (61.47 vs 42.36). Death rate was elevated after mild and after more severe head injury, including in younger adults after mild head injury (14.82 per 1000 per year mild head injury vs 2.21 community). Female gender and greater deprivation were not associated with increased death rates after head injury. Late after injury, deaths occurred from the same main causes as for the general population. Conclusion Head injury is associated with increased vulnerability to death from a variety of causes for at least 13 years after hospital admission. There is a need to understand how head injury influences mortality, particularly in younger adults and after mild head injury.
Analog performance of asymmetric self-cascode p-channel fully depleted SOI transistors

This work presents an analysis of the analog performance of asymmetric threshold voltage self-cascode fully depleted (FD) p-type SOI transistors. The experimental results showed that this structure is able to improve the devices transconductance and output conductance, resulting in increased intrinsic voltage gain and breakdown voltage in comparison to single transistors and the conventional symmetric self-cascode.
Quality care at the end of life in Africa

Each year about 0.5% of the total population in Botswana, Ethiopia, Tanzania, Uganda, and Zimbabwe die from HIV/AIDS or cancer. The members of a WHO project to improve palliative care in these countries discuss their work. The greatest needs of terminally ill patients were for adequate pain relief, accessible and affordable drugs, and financial support to counter the loss of income of both patient and family caregiver. Special emphasis should be given to home based palliative care provided by trained family and community caregivers to counteract the severe shortage of professional healthcare workers Each year in Africa about 2.5 million people die from HIV/AIDS, and more than 0.5 million die from cancer.1 2 Many of these deaths are accompanied by suffering that could be avoided or relieved if adequate palliative care were provided. Quality care at the end of life is a global public health problem.3 4 Palliative care, as defined by the World Health Organization (WHO), is an approach that improves the quality of life of patients and their families facing the problems associated with life threatening illness, through the prevention and relief of suffering by means of early identification and careful assessment and treatment of pain and other problems, physical, psychosocial, and spiritual.2 4 5 Palliative care regards dying as a normal process and offers support to help the patient and family cope during the patient's illness and in the bereavement period. ### What can be done to relieve pain? WHO has developed a relatively inexpensive yet effective method for relieving cancer pain in about 90% of patients6 7 that can be easily extended to patients with HIV/AIDS. Despite this low cost approach, many countries in the developing world provide limited or no palliative care services. A main obstacle is the insufficient availability of opioid drugs because of regulatory and pricing obstacles, …
2 Business processes : the views of the international humanitarian community views

International humanitarian aid provides assistance such as food, shelter, and health or counseling services across national boundaries to communities in need. Universally, international humanitarian aid organizations play a critical role, by supporting the survival and recovery of communities affected by crises such as natural disasters, conflicts or disease epidemics. In most instances the technological, human and financial resources of diverse countries are put together to support communities facing crises. These events, often require immediate action and long term support to sustain the community needs and are highly sensitive to the contexts in which the crisis incidents occur. Large amounts of funds and resources are received each year to support such initiatives and successfully distributing humanitarian aid is a complex operation. Given the size of the funds involved, the sheer complexity and criticality for fast, efficient and effective action in these initiatives, it is somewhat surprising that there is not much evidence of a business process focus by the humanitarian community. This chapter describes the core business of International Non Government Organizations (INGOs), depicts how the main aspects of Business Process Management manifest within INGO’s and points out the values and challenges of process centric approaches within international humanitarian aid organizations. The latter part of the chapter vividly illustrates these aspects using two example cases within the International Federation of Red Cross and Red Crescent Societies.
Self-reported premature ejaculation and aspects of sexual functioning and satisfaction.

BACKGROUND Although premature ejaculation (PE) is a common male sexual dysfunction, its relevant parameters have not been adequately studied in large community-based samples. OBJECTIVE To examine the diagnostic utility of two self-report questions based on the DSM-IV-TR definition of PE and to investigate the relationship between self-identified PE, sexual functioning, and sexual satisfaction in men. METHODS An Internet survey of general health and aspects of sexual functioning and satisfaction was conducted in 2,056 males. Subjects were classified as having "probable" or "possible" PE, or as "non-PE" by survey responses. RESULTS A total of 1158 men met the selection criteria (sexually active in a stable heterosexual relationship), and 189 (16.3%) were classified as having probable PE by reporting they ejaculated before they wished and indicating it was "very much" or "somewhat" a problem. Another 188 (16.2%) men reported ejaculating before they wished but rated their distress lower and were classified as having possible PE. Compared to non-PE men, those with probable and possible PE reported significantly worse sexual functioning in 6 of 8 study measures. Concern about partner satisfaction was high in all groups. The importance of ejaculatory control and the ability to have intercourse for the desired time was significantly higher in men with PE as compared to non-PE men (P < 0.01). CONCLUSIONS PE was a common problem, was characterized by a lack of ejaculatory control, and was associated with significant effects on sexual functioning and satisfaction. Additional research on the sensitivity and specificity of these self-report questions should be pursued.
Jmjd3 activates Mash1 gene in RA‐induced neuronal differentiation of P19 cells

Covalent modifications of histone tails have fundamental roles in chromatin structure and function. Tri‐methyl modification on lysine 27 of histone H3 (H3K27me3) usually correlates with gene repression that plays important roles in cell lineage commitment and development. Mash1 is a basic helix‐loop‐helix regulatory protein that plays a critical role in neurogenesis, where it expresses as an early marker. In this study, we have shown a decreased H3K27me3 accompanying with an increased demethylase of H3K27me3 (Jmjd3) at the promoter of Mash1 can elicit a dramatically efficient expression of Mash1 in RA‐treated P19 cells. Over‐expression of Jmjd3 in P19 cells also significantly enhances the RA‐induced expression and promoter activity of Mash1. By contrast, the mRNA expression and promoter activity of Mash1 are significantly reduced, when Jmjd3 siRNA or dominant negative mutant of Jmjd3 is introduced into the P19 cells. Chromatin immunoprecipitation assays show that Jmjd3 is efficiently recruited to a proximal upstream region of Mash1 promoter that is overlapped with the specific binding site of Hes1 in RA‐induced cells. Moreover, the association between Jmjd3 and Hes1 is shown in a co‐Immunoprecipitation assay. It is thus likely that Jmjd3 is recruited to the Mash1 promoter via Hes1. Our results suggest that the demethylase activity of Jmjd3 and its mediator Hes1 for Mash1 promoter binding are both required for Jmjd3 enhanced efficient expression of Mash1 gene in the early stage of RA‐induced neuronal differentiation of P19 cells. J. Cell. Biochem. 110: 1457–1463, 2010. © 2010 Wiley‐Liss, Inc.