Miracle-dz/UniFAR-FTUs huggingface dataset:
Adverse Drug Reactions Associated with CYP 2B6 Polymorphisms in HIV/AIDS-Treated Patients in Yaoundé, Cameroon

Purpose: The metabolism of antiretroviral drugs is subject to individual variations of the CYP 2B6 gene. The objective of this study was to evaluate the prevalence of CYP 2B6 516 G>T and 983 T>C polymorphisms and investigate their association with the development of adverse drug reactions (ADRs) in people living with HIV/AIDS in Cameroon. Patients and methods: A total number of 122 patients, attending the Yaoundé Central Hospital HIV Day Clinic, consented to take part in this study. Blood specimens were collected and DNA was extracted using the Chelex method. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) was performed for the detection of CYP 2B6 Single-Nucleotide Polymorphisms (SNPs). Genotype frequencies were compared between groups with or without ADRs. Logistic regression analysis was performed to assess association between genotype and adverse effects of antiretroviral therapy (ART). Results: Three types of metabolizers were identi ﬁ ed: extensive, intermediate and slow. For the 516G>T polymorphism, prevalences of 8.2% GG, 65.6% GT and 26.2% TT were obtained. For the 983T>C polymorphism, 89.3% TT, 4.1% CT and 6.6% CC prevalences were obtained. Those homozygous for the wild-type allele (516GG) were less likely to develop ADR with a statistically signi ﬁ cant difference (OR=0.885, P=0.029). For the CYP2B6 T983C SNP, homozygous mutants (CC) may present a higher risk (threefold) of developing adverse reactions (OR=2.677, P=0.164). Conclusion: These ﬁ ndings demonstrate that ADRs among HIV/AIDS patients under ART may be associated with the genetic variability of the metabolizing enzyme CYP 2B6. Genotyping for this gene may guide the better administration of Efavirenz and Nevirapine to Cameroonian patients.
Characterization of Methodologies for the Integrated Assessment of Urban Transportation Sustainabilityª

Objective: To characterize methodologies for the integrated assessment of urban transportation sustainability and to identify research opportunities in developing countries. Materials and methods: A three-stage structured literature review is presented, and a taxonomy is proposed to characterize conceptual frameworks, analytical models, and indices and indicators. An analysis of indicators based on the eleven categories proposed is also presented. Results and discussion: The increase of scientific and institutional literature studying methodologies for sustainability assessment in the last two decades is evidenced. However, the methods still lack the integral inclusion of the economic, environmental, and social dimensions, particularly in the sustainability assessments of urban transportation. Most works are focused on introducting new indices and indicators and applying methodologies in European and North American countries. Conclusions: The characterization identifies the methodologies, institutions, and countries that have implemented methodologies for the integrated assessment of urban transportation sustainability. Likewise, the most frequent sustainability dimensions are identified, and research opportunities in developing countries are outlined.
Conventional and periodic N-grams in the transcription of drum sequences

In this paper, we describe a system for transcribing polyphonic drum sequences from an acoustic signal to a symbolic representation. Low-level signal analysis is done with an acoustic model consisting of a Gaussian mixture model and a support vector machine. For higher-level modelling, periodic N-grams are proposed to construct a "language model" for music, based on the repetitive nature of musical structure. Also, a technique for estimating relatively long N-grams is introduced. The performance of N-grams in the transcription was evaluated using a database of realistic drum sequences from different genres and yielded a performance increase of 7.6 % compared to a the use of only prior (unigram) probabilities with the acoustic model.
1 Structural Disambiguation : Relative-Clause Attachment

In support of a model of language comprehension in which pragmatic biases are integrated with syntactic processing, we show that expectations about upcoming discourse continuations influence the resolution of local structural ambiguity. An off-line sentence-completion study and an online self-paced reading study examined readers’ expectations for high/low relative clause attachments following implicit-causality and non-implicitcausality verbs (John detests/babysits the children of the musician who.). In the off-line study, the widely reported low-attachment preference for English is observed in the non-implicit causality condition, but this preference gives way to more high attachments in the implicit causality condition in cases in which (i) the verb’s causally implicated referent occupies the high-attachment position and (ii) the relative clause provides an explanation for the event described by the matrix clause (e.g., .who are arrogant and rude). In the on-line study, a similar preference for high attachment emerges in the implicit causality context, whereas the low-attachment preference is consistent elsewhere. These results suggest that comprehenders construct discourse contexts dynamically during sentence processing, using available pragmatic cues mid-sentence to generate expectations about the structural analysis of the remainder of the sentence.
Constructing Residential Histories in a General Population-Based Representative Sample

Abstract Research on neighborhoods and health typically measures neighborhood context at a single point in time. However, neighborhood exposures accumulate over the life course, influenced by both residential mobility and neighborhood change, with potential implications for estimating the impact of neighborhoods on health. Commercial databases offer fine-grained longitudinal residential address data that can enrich life-course spatial epidemiology research, and validated methods for reconstructing residential histories from these databases are needed. Our study draws on unique data from a geographically diverse, population-based representative sample of adult Wisconsin residents and the LexisNexis (New York, New York) Accurint, a commercial personal profile database, to develop a systematic and reliable methodology for constructing individual residential histories. Our analysis demonstrated that creating residential histories across diverse geographical contexts is feasible, and it highlights differences in the information obtained from available residential histories by age, education, race/ethnicity, and rural/urban/suburban residency. Researchers should consider potential address data availability and information biases favoring socioeconomically advantaged individuals and their implications for studying health inequalities. Despite these limitations, LexisNexis data can generate varied residential exposure metrics and be linked to contextual data to enrich research into the contextual determinants of health at varied geographic scales.
Maternal blood and amnionic oxytocin receptor gene expression and serum oxytocin levels in preterm birth: a case-control study

BACKGROUND: The oxytocin (OXT)-oxytocin receptor (OXTR) system provides promising candidate gene for studies of genetic contributions to prematurity. OBJECTIVE: Quantification and comparison of oxytocin receptor (OXTR) gene expression and serum OXT levels in the blood and amnion of women delivering preterm and evaluation of the correlation between OXTR gene expression in blood and amnion with serum OXT levels in them. METHODS: 70 pregnant women in spontaneous labor delivering vaginally preterm i.e < 37 weeks and equal number of matched controls delivering spontaneously at term (37-42 weeks) were recruited. Maternal serum OXT levels taken in active stage of labor (i.e 4 cm cervical dilatation) were quantified by ELISA. Gene expression studies in the maternal blood and amnion were done by using real time quantitative polymerase chain reaction (RT-qPCR). RESULTS: The mean serum OXT level in PTL was 48.56 +- 6.97 pg/ml; significantly higher than in controls (43.00 +- 3.96 pg/ml), p<0.001. OXTR gene expression both in maternal blood (2.5 times) and amnion (3.5 times) were significantly higher in PTL. A significant positive correlation was observed between serum OXT levels and OXTR gene expression in amnion (r = -0.190, p = 0.025). CONCLUSIONS: The serum OXT levels and OXTR gene expression in amnion surge significantly in active phase of PTL. Thus, amnion probably links OXT-PTGs autocrine paracrine circuit to facilitate PTL. Future studies are needed to devise better OXTR receptor antagonists preferably acting on amnionic OXTRs to prevent PTL. KEYWORDS: Preterm birth, Preterm labor, Oxytocin, Oxytocin receptor, Placenta, Amnion
a syndrome of severe idiopathic pulmonary parenchymal disease with pulmonary hypertension in Pekingese

: This paper describes 35 Pekingese dogs with a syndrome characterized by dyspnea, cyanosis, episodic syncope, soft pulmonary “velcro” crackles, pulmonary hypertension (PH), and computed tomography and radiographic changes consistent with pulmonary parenchymal disease. The medical data base was searched with the criteria “Pekingese” and “syncope” or “dyspnea” or “tachypnea” or “pulmonary hypertension”, over a 36-month period. Inclusion criteria were echocardiographic changes consistent with noninvasive diagnosis of PH, either subjectively by B-mode or objectively by Doppler. Dogs were excluded (n = 106) if there were insufficient or poor-quality radiographic or echocardiographic records or if diseases other than chronic pulmonary disease were found to be the etiology. The records of 35 dogs met these criteria and presented with a respiratory crises preceded by a history of chronic exercise intolerance and episodic syncope. The average age was 14.5 years (range: 7–19 years), with 21 males and 14 females. Most of the dogs had an interstitial lung pattern with radiographic evidence of right heart enlargement. There was a 77% (n = 27) mortality and a median survival of 60 days (interquartile range: 9–210 days). This study highlights a cor pulmonale syndrome from PH due to chronic pulmonary parenchymal disease, with a grave prognosis, in middle-aged to geriatric population of Hong Kong Pekingese.
Transgene-free, virus-based gene silencing in plants by artificial microRNAs derived from minimal precursors

Abstract Artificial microRNAs (amiRNAs) are highly specific, 21-nucleotide (nt) small RNAs designed to silence target transcripts. In plants, their application as biotechnological tools for functional genomics or crop improvement is limited by the need of transgenically expressing long primary miRNA (pri-miRNA) precursors to produce the amiRNAs in vivo. Here, we analyzed the minimal structural and sequence requirements for producing effective amiRNAs from the widely used, 521-nt long AtMIR390a pri-miRNA from Arabidopsis thaliana. We functionally screened in Nicotiana benthamiana a large collection of constructs transiently expressing amiRNAs against endogenous genes and from artificially shortened MIR390-based precursors and concluded that highly effective and accurately processed amiRNAs can be produced from a chimeric precursor of only 89 nt. This minimal precursor was further validated in A. thaliana transgenic plants expressing amiRNAs against endogenous genes. Remarkably, minimal but not full-length precursors produce authentic amiRNAs and induce widespread gene silencing in N. benthamiana when expressed from an RNA virus, which can be applied into leaves by spraying infectious crude extracts. Our results reveal that the length of amiRNA precursors can be shortened without affecting silencing efficacy, and that viral vectors including minimal amiRNA precursors can be applied in a transgene-free manner to induce whole-plant gene silencing.
Nitrate in the Mississippi River and Its Tributaries, 1980?2010: An Update

Nitrate concentration and flux were estimated from 1980 through 2010 at eight sites in the Mississippi River Basin as part of the National Water-Quality Assessment (NAWQA) Program of the U.S. Geological Survey (USGS). These estimates extend the results from a previous investigation that provided nitrate estimates from 1980 through 2008 at the same sites. From 1980 through 2010, annual flownormalized (FN) nitrate concentration and flux in the Iowa and Illinois Rivers decreased by 11 to 15 percent. These two rivers had the highest FN nitrate concentration in 1980 (5.3 milligrams per liter [mg/L] and 3.9 mg/L, respectively) of any of the study sites. Nitrate increased in the Missouri River (79 and 45 percent increase in FN concentration and flux, respectively), and at the four sites on the Mississippi River (17 to 70 percent increase in FN concentration and 8 to 55 percent increase in FN flux) from 1980 through 2010. Nitrate in the Ohio River was generally stable during this time. Historically, nitrate was high and changed little in the Iowa and Illinois Rivers; however, nitrate concentrations began to decrease around 2000, and this decrease continued through 2010. Also during this time, near-flat nitrate trends in lower sections of the Mississippi River began increasing, likely reflecting the acceleration of http://pubs.usgs. gov/sir/2013/5169/ 11/11/2013 Nitrate in the Mississippi River and Its Tributaries, 1980-2010: An Update Page 2 of 2 already increasing nitrate trends in the upper Mississippi and Missouri Rivers, in addition to increases in inputs from other tributaries in the lower part of the Mississippi River Basin. Spring trends (April through June) generally parallel annual trends at all sites from 1980 through 2010, except in the Iowa River where decreasing nitrate during the spring was not observed. In general, most sites had increases in nitrate concentration at low streamfiows, which suggests increases in legacy nitrate from groundwater or point source contributions. In aggregate, the decreases in nitrate concentrations from the Iowa and Illinois Rivers, which largely occurred during high flows, appear to be overshadowed by increasing nitrate concentrations across much of the Mississippi River Basin.
Andesite, Construction material, Kulon Progo , Yogyakarta, Indonesia.

The construction projects that are currently being carried out in Kulon ProgoRegency, Yogyakarta Special Province, Indonesia, started on 2018, are large-scale projects. The projects include the construction of airports, seaports, industrial estates, southern crossing lanes and the construction of Menoreh lanes. The large-scale projects require a very large supply of andesite rocks for material construction. In Kulon Progo Regency itself, there is a huge potential of andesite rock relate to two geological formations (Kebo Butak and Andesite Intrusion) exist in the region, which is found mostly in Kokap District and partly in Temon District. One parameter that determines the quality of andesite rock is their compressive strength. Due to weathering, not all of the andesite in both formation can be classified as good quality rocks. According to Indonesian Standard, theminimum compressive strength of natural stone for stakes and curbstone is 500 kg/cm2 , for lightweight building foundation is 800 kg/cm2 , for medium building foundations is 1000 kg/cm 2and for heavy building foundations is 1500 kg/cm 2 . Based on this background, this paper have objectives to know the quality of andesite rock exist in the research area and to determine the zonation of good quality andesite rock for building androad materials in the research area. Field observation were conducted to map the occurrence of andesite rock. Totally 68 rock samples were collected during field observation and tested by point load test method to know its compressive strength value. The distribution of good quality rock in the research area were determine based on spatial analysis procedure in geographical information system. Results show that andesite rocks found in research area have a compressive strength ranging from 167.12 kg/cm 2 to 2783.37 kg/cm 2 . From 53 samples taken from igneous rock intrusion, it showed that 7.55 % had low quality, 13.21 % had medium quality, 30.19 % had good quality and 49.06 % had very good quality. From the 16 samples taken from the Kebobutak Formation, it showed that 12.50 % had low quality, 18.75 % had good quality and 67.75 % had very good quality. The final map of rock quality zonation reveals 28.92 % of research area classify as low quality, 2.52 %medium quality, 37.68 % good quality and 30.88 % very good quality. It can be concluded that almost 70 % of andesite in the Kokap and Temon District can be used for the running large scale projects.
The impact of the temporal sequence of cranial radiotherapy and platin‐based chemotherapy on hearing impairment in pediatric and adolescent CNS and head‐and‐neck cancer patients: A report from the PanCareLIFE consortium

The impact of the temporal sequence by which cranial radiotherapy (CRT) and platin‐based chemotherapy (PCth) are administered on sensorineural hearing loss (SNHL) in pediatric and adolescent central nervous system (CNS) and head‐and‐neck (HN) cancer patients has not yet been studied in detail. We examined the ototoxic effects of sequentially applied CRT and PCth. This study included children and adolescents with CNS and HN tumors who participated in the multicountry PanCareLIFE (PCL) consortium. Audiological outcomes were compared between patients who received CRT prior to PCth and those who received it afterwards. The incidence, degree and posttreatment progression of SNHL, defined as Muenster classification grade ≥MS2b, were evaluated in 141 patients. One hundred and nineteen patients were included in a time‐to‐onset analysis. Eighty‐eight patients received CRT prior to PCth (Group 1) and 53 patients received PCth before CRT (Group 2). Over a median follow‐up time of 1.6 years, 72.7% of patients in Group 1 experienced SNHL ≥ MS2b compared to 33.9% in Group 2 (P < .01). A time‐to‐onset analysis was performed for 74 patients from Group 1 and 45 patients from Group 2. Median time to hearing loss (HL) ≥ MS2b was 1.2 years in Group 1 and 4.4 years in Group 2 (P < .01). Thus, audiological outcomes were better for patients who received CRT after PCth than before. This finding should be further evaluated and considered within clinical practice in order to minimize hearing loss in children and adolescents with CNS and HN tumors.
Sublobar resection reduces the risk of postoperative cognitive dysfunction compared with lobectomy

Abstract OBJECTIVES Sublobar resection, including wedge resection and segmentectomy, is non-inferior to lobectomy in early-stage non-small cell lung cancer treatment. We aimed to compare the risk of postoperative cognitive dysfunction (POCD) between sublobar resection and lobectomy. METHODS We conducted a prospective cohort study. Patients with sublobar resection or lobectomy were divided into the sublobar group or the lobar group, respectively. Cognition was assessed before and after surgery with Montreal Cognitive Assessment and Minimum Mental State Examination tests. POCD is defined as Z score of Montreal Cognitive Assessment change ≤–1.96. Propensity score matching (PSM) was performed to make demographics well-balanced between the 2 groups. RESULTS A total of 335 patients were enrolled. Both the postoperative 1-day POCD rate (sublobar 5.5% vs lobar 18.2%, P < 0.001) and the postoperative 1-month POCD rate (sublobar 7.9% vs lobar 21.8%, P < 0.001) were significantly lower in the sublobar group compared with lobar group, with demographics unbalanced between the 2 groups. In the 133 demographics-matched pairs obtained by PSM, both the postoperative 1-day POCD rate (sublobar 5.3% vs lobar 17.3%, P = 0.005) and the postoperative 1-month POCD rate (sublobar 8.3% vs lobar 18.8%, P = 0.018) remained significantly lower in the sublobar group than in the lobar group. The incidences of postoperative 1-day (P = 0.109) and postoperative 1-month (P = 0.026) Minimum Mental State Examination abnormity were also lower in the sublobar group than in the lobar group but only the latter was with statistical significance after PSM. CONCLUSIONS Sublobar resection has an advantage over lobectomy in preventing POCD. Our findings might be a reference for selecting the most suitable type of resection for non-small-cell lung cancer patients.
Randomized controlled trial

Objectives Flexible sigmoidoscopy (FS) screening at around age 60 can reduce the incidence of colorectal cancer (CRC). Insufficient evidence exists on FS at 60 years in a population being offered biennial faecal occult blood test (FOBT) screening from 50 years. A randomised controlled trial (RCT) assessed if FS would be an effective adjunct to FOBT.
Nanomaterial genotoxicity evaluation using the high-throughput p53-binding protein 1 (53BP1) assay

Toxicity evaluation of engineered nanomaterials is challenging due to the ever increasing number of materials and because nanomaterials (NMs) frequently interfere with commonly used assays. Hence, there is a need for robust, high-throughput assays with which to assess their hazard potential. The present study aimed at evaluating the applicability of a genotoxicity assay based on the immunostaining and foci counting of the DNA repair protein 53BP1 (p53-binding protein 1), in a high-throughput format, for NM genotoxicity assessment. For benchmarking purposes, we first applied the assay to a set of eight known genotoxic agents, as well as X-ray irradiation (1 Gy). Then, a panel of NMs and nanobiomaterials (NBMs) was evaluated with respect to their impact on cell viability and genotoxicity, and to their potential to induce reactive oxygen species (ROS) production. The genotoxicity recorded using the 53BP1 assay was confirmed using the micronucleus assay, also scored via automated (high-throughput) microscopy. The 53BP1 assay successfully identified genotoxic compounds on the HCT116 human intestinal cell line. None of the tested NMs showed any genotoxicity using the 53BP1 assay, except the positive control consisting in (CoO)(NiO) NMs, while only TiO2 NMs showed positive outcome in the micronucleus assay. Only Fe3O4 NMs caused significant elevation of ROS, not correlated to DNA damage. Therefore, owing to its adequate predictivity of the genotoxicity of most of the tested benchmark substance and its ease of implementation in a high throughput format, the 53BP1 assay could be proposed as a complementary high-throughput screening genotoxicity assay, in the context of the development of New Approach Methodologies.
A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species

Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like Bos species, as well as 0.6% of unknown origin. Introgression from multiple donors might have contributed to the genetic diversity of Chinese indicine cattle. Altogether, this study highlights the contribution of interspecies introgression to the genomic architecture of an important livestock population and shows how exotic genomic elements can contribute to the genetic variation available for selection.