dataesr/scientific-paragraphs-categorization huggingface dataset:
Introduction: We aimed to describe the frequency of CD4 and VL monitoring for HIV-positive patients (HIV ' ) receiving antiretroviral therapy (ART) in Latin America and the Caribbean, assess adherence to recommendations in clinical guidelines, identify factors associated with lower frequency of monitoring and describe costs of monitoring patients on ART. Methods: We used retrospective cohort data from all CCASAnet sites during 2000Á2012. Patients initiating ART were included. Followup time after ART initiation was divided into 180-day periods. The primary outcome was the proportion of 180-day periods with adequate monitoring, defined as having at least one CD4 and one VL measurement. In secondary analyses, adequate monitoring was based only on CD4. Factors associated with monitoring frequency were assessed using multivariable Poisson regression models, with the number of 180-day periods with adequate monitoring as outcome.
Median cost for CD4 and VL measurements per patient/year were estimated. Results: A total of 14,476 patients were included. Median follow-up time was 50. 4 months (IQR: 27Á82. 3). CD4 were monitored from a median of 2. 6 measurements/year for CMH-Argentina to 1. 0/year for GHESKIO-Haiti; VL measurements ranged from 2. 6/year for CMH-Argentina and INCMNSZ-Mexico to 0. 9/year for IHSS/HE-Honduras; VL was not regularly measured at GHESKIO-Haiti. The mean proportion of periods with adequate CD4 and VL monitoring was 61. 7% (95% CI: 52. 3Á72. 8), ranging from 85. 6% at INCMNSZ-Mexico to 25. 6% at IHSS/HE-Honduras. The mean proportion of 180-day periods with adequate CD4 monitoring alone was 68. 6% (95% CI: 57. 5Á81. 8%). Rates ranged from 86. 5% at INCMNSZ-Mexico to 48. 2% at GHESKIO-Haiti. We will show in figures in the presented data the factors associated with adequate monitoring expressed in OR: increased age, and more recent initiation of ART, which were consistently positively associated with adequate monitoring.
The sample consisted of 100 participants meeting the CDC case definition for CHIKV infection. Random distribution of cases (HIV negative) and controls (HIV positive) were allocated based on HIV known status at the moment of presenting to care. After informed consent IgM antibodies were identified to differentiate dengue from CHIKV infections. CD4' T lymphocytes and HIV viral load, and HIV medications were reviewed. Epidemiological data was analyzed with Epi Info TM 7. Results: A total of 100 participants fulfilled inclusion criteria. Distribution of cases and controls was 1:1. Men constituted 23% (n0 23) of total sample. The mean age for men was 44. 04 years (SD 00. 5), and for women 45. 29 years (SD 01. 1). Immune status of HIV-positive participants assessed by CD4' T lymphocytes revealed that 76.
To describe the main risk behaviours for HIV-infection, its control, the prevalence of comorbidities and other co-infections in prisoners who were treated in the HIV-Unit of Hospital Civil de Guadalajara, Mexico. All HIV-infected prisoners who were receiving medical care at our HIV-unit from May 1st 2013 to May 31st 2014 were included. Data were obtained from an electronic database of medical records. Results: A total of 88 patients were included, 95% were male, with a median age of 36 years, all Hispanic. The principal risk factors to HIVinfection were unprotected heterosexual intercourse (55%), following of homo/bisexual intercourse, intravenous drug use (45 and 33%, respectively). The 71% of patients were in an advanced stage of HIV infection and 72% of the patients on HIV-treatment, reached HIV control with undetectable viral load.
Introduction: The infection of the human papilloma virus (HPV) of high risk (HR) is a necessary factor for cervical lesions and invasive cervical cancer (ICC)  [1]. In women with human immunodeficiency virus (HIV), HPV infections are more frequent with a higher risk of ICC  [2, 3]. Materials and methods: Learn the HPV (HR) and cervical lesions prevalence, describing the distribution of different genotypes, and the epidemiologic clinical characteristics of women co-infected with HIV and HPV (HR). Identify the cytological characteristics in HIV-positive women that frequent the Condesa Specialised Clinic in Mexico City. The cohort was made up of 401 HIV-positive women. The women had a gynaecological exploration, cervical cytology, colposcopy and HPV typfication, and biopsy if necessary. The data was obtained through questionnaires with socio-demographic, behavioural and clinical variables.
1 software was used  [2]. For analysis of HIV-1 subtypes and their CRFs the software of the National Center for Biotechnology Information (NCBI) was employed, using the database Genotyping Reference Dataset (Human Immunodeficiency Virus (HIV-1)) ''pure'' & CRFs 2005  [3]. The subtypes and recombinant forms were confirmed using the REGA HIV-1 Subtyping Tool software  [4, 5]. Results: We genotyped and analyzed a total of 301 samples from HIV-1 positive Colombian patients, with failure to antiretroviral therapy. Geographical distribution of the samples: 23 (7. 6%) from Bogota, 123 (40. 9%) from Medellin, 135 (44. 9%) from Cali and 20 (6. 6%) from Barranquilla. In Colombia subtype B was found in 245 (81. 4%) of the cases. The recombinant subtype D/B was identified in two cases (0. 66%) and six different CRFs from 54 patients were distributed as: 1 (0.
Introduction: The introduction of highly active antiretroviral therapy (HAART) has significantly improved life expectancy on HIV-infected subjects and the population is becoming older. The CDC considers elderly HIV-patients at the age ]50 years due to the impact of HIV-infection per se and the use of antiretrovirals  [1]. Information regarding the elderly-infected population is still limited. The aim of this study was to describe the profile in a cohort of patients ]50 years followed-up in a HIV-care at Guadalajara, Mexico. Materials and methods: Patients were retrospectively analyzed at the HIV-unit in Hospital Civil de Guadalajara. Patients ]50 years currently being followed-up at the site were included. Data were obtained from an electronic database. Significance level was established 55%.
Introduction: The success of high activity antiretroviral therapy (HAART) is associated with the ''ageing'' of the HIV epidemic  [1]. In Mexico 15. 7% of people living with HIV (PLH) receiving HAART at the Mexican Health Department (MHD) are aged 50 years or older  [2]. Health-care delivery systems must be ready to provide quality integral treatment to PLH, making it necessary to study the different cardiovascular risk factors among this particular population  [3, 4]. Material and methods: A cross-sectional study was conducted using a database built from chart review and laboratory's database of Condesa Clinic with data from 2009 to 2012. The clinic is in Mexico City and is the largest clinic in Mexico. The objective was to describe the prevalence of cardiovascular risk factors in PLH in HAART age 20 years or older.
Age, gender, time since diagnosis, high blood pressure (BHP, SP]140 mmHg, DP]90 mmHg), diabetes mellitus (DM ]126 mg/d), hypercholesterolemia ( ]200 mg/dl), hypertriglyceridemia ( ]150 mg/dl), smoking and obesity (BMI ]30 kg/m 2 ) and Framingham risk score were studied. Gender was categorized in men, women and transwomen. The database was validated and analyzed using Stata11. Results: A total of 904 men, 64 women and 28 transwomen were analyzed. Mean age was 36. 5 (95% CIs 35. 9Á37. 1), glucose level 96. 8 mg/dl (95% CIs 95. 2Á98. 5), cholesterol 171. 5 mg/dl (95% CIs 168. 3Á174. 7), HDL 37. 8 mg/dl (95% CIs 37. 0Á38. 6), triglycerides 239. 3 mg/dl (95% CIs 227. 8Á250. 9). Framingham risk score was 4. 9% (95% CIs 4. 6Á5. 1). BMI significantly increased 1. 8 kg/m 2 (95% CIs 1. 7Á2. 1). Prevalence were hypercholesterolemia 25.
Having HIV patients concentrated in the same place with supervised ARV daily dosage intake results in better adherence, retention in care and thus better virology control decreasing infection probability. Materials and methods: It is a retrospective study. We used data from the National System for Logistics Administration and Surveillance of ARV in Mexico (SALVAR in Spanish) up to the 31 December 2014, the database of the CIENI/CENSIDA and the database of the HIV Prison Programme in Mexico City. Criteria for inclusion: Incarcerated male patients with HIV infection in Mexico City during 2014 in Santa Martha Acatitla Penitentiary. Results: We started 2014 with 184 patients, adding 60 new patients throughout the year, 13 recidivists, 67 were freed and 9 died. At 31 December 2014, 206 HIV patients remained incarcerated, of which 92.
The clinical implications Abstracts of the HIV Drug Therapy in the Americas Journal of the International AIDS Society 2015, 18 (Suppl 2)Abstracts of the HIV Drug Therapy in the Americas Journal of the International AIDS Society 2015, 18 (Suppl 2) Materials and methods: We conducted a retrospective cohort study, which included 16 children with virological failure and triple-class drug HIV resistance HIV-1 infection. All patients had protease and retrotranscriptase genotype, and they were evaluated using the Stanford HIV database for resistance mutation interpretation. Switch of antiretroviral (ARV) regimen was based on genotyping data, evaluated by an experts group in antiretroviral drugs resistance. The primary end point was virologic suppression ( B50 copies/ml) and immunologic improvement at Week 24.
Neutrophil isolation Neutrophil purification was performed as previously described  [16] , with modifications. Briefly, peripheral blood was obtained from HIV-1(+), HESN and controls, by venipuncture into tubes containing ACD anti-coagulant (BD Pharmingen, San Diego, CA). The red cells were precipitated by adding dextran (Sigma-Aldrich Chemical Co. , St. Louis, MO) in 0. 9 M NaCl and incubating 50 min at 4°C, and the upper phase which corresponds to leukocyte-rich plasma was collected. The pellet underwent lysis of the remaining red blood cells followed by density gradient centrifugation with Ficoll-Hypaque 1077 (Sigma-Aldrich Chemical Co. ). The neutrophils were re-suspended in RPMI1640 (BioWhittaker, Walkersville, MD) enriched with 10% heat-inactivated fetal bovine serum (FBS). This protocol yielded neutrophils that were 94-96% pure, 98-99% viable and without basal activation, measured by IL-6 production (data not shown).
Flow cytometry analysis Flow cytometry was used to evaluate the effect of HIV-1 infection on the expression of TLR2, TLR4, CD62L and CD11b on neutrophils. For this purpose, freshly isolated neutrophils were surface-stained with the appropriate antibodies for 25 min; the acquisition was performed immediately using a FACSCan flow cytometer (BD Biosciences, San Jose, CA). The acquired events were analysed using FACS Diva software version 6. 1. 2. Receptor expression is expressed as the mean fluorescent intensity (MFI) of the overall cell sub-population after subtraction of the isotype control. RNA isolation, cDNA synthesis and quantitative real-time PCR for PRR and cytokine mRNAs mRNA quantification for cytokines (IL-6, TNF-α, IL-1β, IL-18 and TGF-β) and PRR (TLR2, TLR4, TLR7, TLR8, TLR9, RIG-I, MDA-5, NOD1, NOD2, NLRP1 and NLRC4) was performed in neutrophils from HIV-1(+), HESN and controls.
Statistical analysis Data were plotted and analyzed using the Prism 5. 0 software (Graph Pad Software, CA). The results of the in vitro assays represent all the data collected from patients, cultured in duplicates. Unpaired two-tailed student t-tests (Mann-Whitney U-tests) and ANOVA tests were used to assess the statistical significance of PRR expression or function in the different groups, when data from more than three independent experiments were available. Values of p<0. 05 ( Ã ) and p<0. 01 ( ÃÃ ) were considered statistically significant.
Absence of neutropenia in HESN individuals Early asymptomatic HIV-1 infection and advanced HIV-1-related immunodeficiency are associated with neutropenia  [18]. No significant differences were observed when the number or percentage of neutrophils was evaluated among the groups of donors. (data not shown). Moreover, HESN have significantly higher CD4 + T-cell, mDC and pDC counts compared with HIV-1(+) (data not shown).
Measurements, all in micrometers, were taken following the procedures of  MIZELLE & KLUCKA (1953). In the descriptions, the mean is followed by the range and the number of structures measured (n), in parentheses; the length of the body includes the haptor (longitudinal axis of haptor). The length of the male copulatory organ (MCO) and bars represent their actual length measured with the software ImageJ  (SCHNEIDER et al. 2012 ). The hooks are numbered according to  MIZELLE (1936)  Vitellaria in trunk, absent from regions of other reproductive organs. Haptor bifurcated, composed by bilateral "arms"; with dorsal, ventral anchor/bar complexes, seven pairs of similar hooks (5 pairs ventral, 2 pairs dorsal). Hook with shank comprising single subunit. Bars elongate, inverted U-shaped. Ventral anchor with elongate deep root.
Design and Manufactured Prototype The first step in designing the matrix antenna is the modeling of the EBG pixel. Figure  1  shows the EBG pixel design using full-wave simulation software (CST Microwave Studio). As described in  [7] , the pixel is a resonant cavity formed between a ground plane and a FSS placed above it in the  direction and surrounded by four metallic walls. The FSS is composed of a centered and periodic assembly of 9 square patches (4 × 4 mm 2 ) directly printed at the bottom of the FSS dielectric substrate (RO4003C by Rogers). Figure  2 (a) shows the dimensions of the printed FSS in detail. This FSS presents a negative reflection phase value  [8, 9]  which makes the cavity height lower than  0 /30, as shown in Figure  2 (b) (cavity height = 1 mm,  0 = 8. 2 GHz, pixel bandwidth = 5%).
5cm. For the qualitative analysis of the data, we provide to the botanist team different georeferenced products computed from the data acquired by the tri-cam payload. These products were high resolution orthomosaics, unsupervised automatic classification using Maximum Likelihood Estimation algorithm  (Data et al. , 2008)  and 3D reconstructions. From the High Resolution orthomosaic (1. 5cm GSD), the botanists made the classification manually (figure  10 ) and compare the results with their own last cartography of the site realized in-situ. The qualitative analysis shows that they have been able to identify four different species on the seven ones really living on the area. The global land-cover obtained is identical on about 62% with ground measurements 92% of tree higher than 1 meter has been identified.
Crystallization and structure determination Both native and SeMet-substituted Cgi121 proteins were stored in 20 mM Tris-HCl pH 7. 5, 300 mM NaCl, 5 mM 2-mercaptoethanol. Crystals were grown at 20 • C from a 0. 5:0. 5 l mixture of a 15-mg/ml protein solution with a crystallization solution composed of 1. 2 M sodium citrate, 0. 1 M sodium citrate pH 5. For data collection, the crystals were directly flash-frozen in liquid nitrogen. The native and SeMet diffraction data were recorded on beamlines ID14-EH1 and BM30A, respectively (ESRF, Grenoble, France). The structure was determined by the SAD method (Single wavelength Anomalous Dispersion) using the anomalous signal from the selenium element. Data were processed using the XDS package  (27). The space group was P2 1 2 1 2 1 with two copies per asymmetric unit.
All the expected Se sites (five per monomer) were found with the program SHELXD using reflections in the 50-3 Å resolution range  (28). Refinement of the Se atom positions, phasing and density modification were performed with the program SHARP  (29). The quality of the experimental phases allowed automatic building of an almost complete model with the ARP/WARP application  (30, 31). This model was then refined against the 1. 9 Å native data set using PHENIX  (32)  and then rebuilt with the 'TURBO' molecular modeling program (http://www. afmb. univ-mrs. fr/-TURBO). The final model contains residues 1-177 and 1-178 from monomers A and B, respectively. In addition, 383 water molecules could be modeled into the electron density maps. Statistics for all the data collections and refinement of the SeMet-substituted and native Cgi121 are summarized in Supplementary Table  S1.
Bud32-Cgi121-6His was crystallized using the hanging drop vapor diffusion method. Crystals were obtained at 20 • C from a crystallization solution that contains Bud32-Cgi121-6His at 5 mg/ml in 50 mM Tri-sodium pH 5. 6, 10% 2-Propanol and 10% PEG4000 or 50 mM sodium acetate pH 4. 6, 1 M ammonium sulfate. The crystals were cryo-protected by transfer into the crystallization solution with increasing glycerol concentrations up to 30% v/v and then flash cooled in liquid nitrogen. The diffraction data set was collected at SOLEIL Synchrotron beamline Proxima 1 (Saint Aubin, France). Data were processed using the XDS package  (27). The space group was I4 1 with one heterodimer per asymmetric unit. The structure was determined by the molecular replacement method with the program MOLREP (33), using SeMet-substituted Cgi121 and Methanocaldococcus jannaschii Bud32 (15) structures as search models.
The native and SAD data sets were collected at 100 K on the SOLEIL Synchrotron beamline Proxima 1 (Saint Aubin, France). The native and SeMet-substituted data sets were processed at 3. 0 Å and 2. 5 Å, respectively, with the XDS package  (37). Both complexes crystallized in the space group C2 with three copies of the Pcc1-Gon7 complex in the asymmetric unit (cell parameters are summarized in Table  1 ). The structure of the SeMet-substituted Pcc1-Gon7 complex was determined by the SAD method. Nine selenium sites (six from Pcc1 and three from Gon7) out of a total of 18 were located using the program SHELXD  (38). The phasing and the refinement of the Se sites were performed with Phaser (39) and Parrot  (40) , respectively. The model building was carried out with the Buccaneer package  (41)  and the COOT (36) program, taking advantage of the structural model of Pyrococcus furiosus Pcc1  (17).
Small angle x-ray scattering Small angle x-ray scattering (SAXS) experiments were carried out at the SOLEIL synchrotron SWING beamline (Saint-Aubin, France). The sample to detector (Aviex CCD) distance was set to 1500 mm, allowing reliable data collection over the momentum transfer range 0. 008 Å-1 < q < 0. 5 Å-1 with q = 4sin/, where 2 is the scattering angle and is the wavelength of the X-rays ( = 1. 0 Å). In order to separate the various species in solution, SAXS data were collected on samples eluting from an online sizeexclusion high-performance liquid chromatography (SE-HPLCBio-SEC3 Agilent) column available on SWING and directly connected to the SAXS measuring cell. The purified KEOPS or Pcc1-Gon7 complexes were injected in the column pre-equilibrated with preparative buffer comprising 20 mM Tris pH 7.
5, 200 mM NaCl and 5 mM 2mercaptoethanol. Flow rate was 200 l/min, frame duration was 1. 0 s and the dead time between frames was 0. 5 s. For each frame, the protein concentration (between 0. 5 and 2. 0 mg/ml at the top of elution peak) was estimated from UV absorption at 280 and 295 nm using a spectrometer located immediately upstream of the SAXS measuring cell. Selected identical frames corresponding to each elution peak were averaged. A large number of frames were collected before the void volume and averaged to account for buffer scattering. SAXS data were normalized to the intensity of the incident beam and background (i. e. the elution buffer) substracted using the programs FoxTrot (courtesy of SWING beamline) and Primus  (43, 44). The scattered intensities were displayed on an absolute scale using the scattering by water.
Gon7/Pcc1 in solution Sequence-based structure prediction indicates that Gon7 is almost fully disordered (Supplementary Figure  S2A ). Since more than half of the Gon7 protein was not observed in the crystal, we investigated whether Gon7 becomes partially structured upon complex formation with Pcc1. We therefore prepared N 15 -labeled Gon7 and investigated the folding of the construct by nuclear magnetic resonance (NMR). The HSQC spectrum of Gon7 shows that the protein alone in solution is unstructured (Supplementary Figure  S2B ). We attempted to titrate N 15 -labeled Gon7 with unlabeled Pcc1, but the latter protein forms stable soluble high molecular weight aggregates when produced alone and hence did not affect the HSQC spectrum of Gon7 (data not shown). We then examined the oligomerization state of the Gon7/Pcc1 complex in solution by SEC-MALLS.
We examined the structure of the Gon7/Pcc1 complex in solution by SAXS. The X-ray scattering curves are presented in Supplementary Figure  S3A  and structural parameters summarized in Supplementary Table  S2. The experiments were performed using a gel filtration column coupled to the SAXS instrument  (46). SAXS data were collected online throughout the elution time. Selected identical scattering curves corresponding to the start of the elution peak were averaged. The value of the molar mass M obtained from the complete I(q) curve (M = 51 ± 5 kDa) is compatible with the calculated mass of the Gon7/Pcc1 heterotetramer (M calc = 48. 8 kDa). Unfortunately, the SAXS data do not allow choosing between the two types of heterotetramers (Supplementary Figure  S3B  and D ), as both can be equally well incorporated within the envelope of the complex deduced from the SAXS curve using the program GAS-BOR  (47).
Upon superposition of the N-terminal lobes of yeast and archaeal Bud32, their Cterminal lobes are slightly shifted (data not shown). The structure of the M. jannaschii Kae1/Bud32 complex was determined in the presence of the nucleotide analog AMPPNP. Although the electron density for AMPPNP was clearly defined in the active site of Kae1, it was absent from Bud32  (16). Likewise, no binding of nucleotide was observed in Bud32 in the structure of the ternary Kae1/Bud32/Cgi121 complex from archaea  (17). We cocrystallized yeast Bud32/Cgi121 in the presence of ATP, ADP, AMPPNP and AMP and in all cases the nucleotide was well bound at the active site of Bud32 (Supplementary Figure  S5 ). The adenosine base occupies a hydrophobic pocket created by residues of the linker region between the two lobes.
7 kDa), suggesting yeast KEOPS forms a hetero-pentamer in solution. In order to confirm the stoichiometry and to evaluate our model of the complex, we investigated the intact KEOPS complex in solution by SAXS coupled to gel filtration. The molar mass extracted from the scattering curve corresponding to the top of the elution peak is equal to 122 ± 10 kD (Supplementary Table  S2 ), in good agreement with the SEC-MALLS results. We evaluated our above-mentioned linear model of the yeast KEOPS complex against the SAXS data. The program BUNCH  (49)  was used for modeling the missing parts of the model (mainly in the Gon7 subunit) as chains of dummy residues whose C-alpha positions are separated by 3. 8 Å. Reconstructing the backbone and adding the side chains using the program PD2  (50)  then completed the model.
The scattering amplitude curves calculated on the final model by using the program CRYSOL (  51 ) is in good agreement with the experimental curve (χ = 1. 25) (Figure  4B ). These data validate the quaternary structure and the molecular architecture of our model of yeast KEOPS. It was shown that the five KEOPS subunits are required for the biosynthesis of tRNA t 6 A (6,8) and that Kae1 transfers the threonylcarbamoyl moiety from TCA onto substrate tRNA  (6, 9). In our model, the catalytic center of Kae1 contacts the C-terminal region of Bud32 and Pcc1 and Gon7 surround the active site entrance. The bottom of the crater formed by Gon7-Pcc1-Kae1-Bud32 has a positively charged and conserved surface (Figures  3  and 5 ). After refinement of the Bud32-Cgi121 structure we observed residual electron density for four sulphate ions.