Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial Modelling to Inform Public Health Based on Health Surveys: Impact of Unsampled Areas at Lower Geographical Scale

Small area estimation is an important tool to provide area-specific estimates of population characteristics for governmental organizations in the context of education, public health and care. However, many demographic and health surveys are unrepresentative at a small geographical level, as often areas at a lower level are not included in the sample due to financial or logistical reasons. In this paper, we investigated (1) the effect of these unsampled areas on a variety of design-based and hierarchical model-based estimates and (2) the benefits of using auxiliary information in the estimation process by means of an extensive simulation study. The results showed the benefits of hierarchical spatial smoothing models towards obtaining more reliable estimates for areas at the lowest geographical level in case a spatial trend is present in the data. Furthermore, the importance of auxiliary information was highlighted, especially for geographical areas that were not included in the sample. Methods are illustrated on the 2008 Mozambique Poverty and Social Impact Analysis survey, with interest in the district-specific prevalence of school attendance.
Effects of mesalazine combined with bifid triple viable on intestinal flora, immunoglobulin and levels of cal, MMP-9, and MPO in feces of patients with ulcerative colitis.

OBJECTIVE Ulcerative colitis (UC) commonly occurs in young and middle-aged people and is characterized by frequent attacks and difficult cure. Mesalazine is often applied in the initial treatment of UC, but it can lead to serious adverse effects. Its combination with bifid triple viable could mitigate adverse effects. This study aims to explore the effects of mesalazine combined with bifid triple viable on the intestinal flora, immunoglobulin (Ig), and levels of calprotectin (Cal), matrix metalloproteinase-9 (MMP-9), myeloperoxidase (MPO) in feces of UC patients. PATIENTS AND METHODS A total of 180 UC patients in our hospital were divided into two groups with 90 cases in each one. Patients in control group were treated with oral mesalazine (1.5 g/d), and those in the treatment group were treated with oral mesalazine (1.5 g/d) combined with bifid triple viable (1.26 g/d) for 2 months. Treatment effects in both groups following the therapeutic period were observed accordingly. Feces of patients in the two groups were collected for detecting intestinal microorganism and the levels of Cal, MMP-9, and MPO. Serum levels of IgG, IgA, and IgM in each patient were detected by enzyme-linked immunosorbent assay (ELISA). RESULTS The overall response rate of the treatment group (91.11%) was significantly higher than that of control group (68.89%; p=0.000). The abundances of intestinal microflora, including Bifidobacterium, Actinomycetes, Rikenellaceae, Genus VI of Acidaminococcaceae, and Metascardovia in treatment group were remarkably higher than those in control group. The abundances of intestinal microorganisms such as Phocaeicola, Lawsonia intracelluaris, Streptococcus, Ruminococcaceae, and Clostridium in control group were significantly higher than those in treatment group. After treatment, serum levels of IgG and IgM of patients in treatment group were lower than those in control group, with IgG of (15.14±0.98) (p=0.031) and IgM of (1.50±0.18) (p=0.000). No statistical difference in IgG level was observed between treatment group and control group after treatment (p=0.871). After treatment, the levels of Cal and MMP-9 in feces of patients in treatment group were significantly lower than those in control group with Cal of (79.81±5.42) (p=0.000) and MMP-9 of (4.89±0.98) (p=0.000). There was no statistical difference in the MPO level between treatment group and control group after treatment (p=0.871). CONCLUSIONS Mesalazine combined with bifid triple viable is able to enhance the curative effect for UC, improve the composition of intestinal flora, weaken the immune response, and reduce levels of Cal and MMP-9 in the intestinal tract.
Validation of the RumiWatch Converter V0.7.4.5 classification accuracy for the automatic monitoring of behavioural characteristics in dairy cows

ABSTRACT The objective of the present study was to validate the accuracy of algorithms, implemented in the currently available RumiWatch Converter (RWC) version V0.7. 4.5 of the RumiWatch System (RWS), for the classification of behavioural characteristics from jaw and head movements which are monitored by a noseband halter comprising a pressure sensor and a triaxial accelerometer. The accurate classification of behavioural characteristics in different time resolutions is critical for the usage of the RWS for scientific and practical purposes as chewing behaviour provides essential indicators for the assessment of diet adequacy in dairy cows. To validate the RWC V0.7. 4.5 classification accuracy for behavioural characteristics of rumination, eating, drinking, other activity and ruminating chews per bolus by direct observation as reference method, 14 dairy cows participated in the trial. Concordance between the consolidated 1-min and 1-h classification results was assessed. The RWC V0.7. 4.5 classified only rumination and ruminating chews per bolus precisely, whereas an algorithm optimisation for the classification of eating, drinking and other activity is required. Additionally, classification results from the 1-min and 1-h time summaries were not in agreement with each other except for rumination.
Global reforestation and biodiversity conservation

The loss of forest is a leading cause of species extinction, and reforestation is 1 of 2 established interventions for reversing this loss. However, the role of reforestation for biodiversity conservation remains debated, and lacking is an assessment of the potential contribution that reforestation could make to biodiversity conservation globally. We conducted a spatial analysis of overlap between 1,550 forest‐obligate threatened species’ ranges and land that could be reforested after accounting for socioeconomic and ecological constraints. Reforestation on at least 43% (∼369 million ha) of reforestable area was predicted to potentially benefit threatened vertebrates. This is approximately 15% of the total area where threatened vertebrates occur. The greatest opportunities for conserving threatened vertebrate species are in the tropics, particularly Brazil and Indonesia. Although reforestation is not a substitute for forest conservation, and most of the area containing threatened vertebrates remains forested, our results highlight the need for global conservation strategies to recognize the potentially significant contribution that reforestation could make to biodiversity conservation. If implemented, reforestation of ∼369 million ha would also contribute substantially to climate‐change mitigation, offering a way to achieve multiple sustainability commitments at once. Countries must now work to overcome key barriers (e.g., unclear revenue streams, high transaction costs) to investment in reforestation.
Fosamprenavir with Ritonavir Pharmacokinetics during Pregnancy

The purpose of this study was to evaluate the pharmacokinetics of ritonavir-boosted fosamprenavir during pregnancy and postpartum. Amprenavir (the active moiety of fosamprenavir) and ritonavir intensive pharmacokinetic evaluations were performed at steady state during the second and third trimesters of pregnancy and postpartum. Plasma concentrations of amprenavir and ritonavir were measured using high-performance liquid chromatography. The target amprenavir area under the concentration-versus-time curve (AUC) was higher than the 10th percentile (27. ABSTRACT The purpose of this study was to evaluate the pharmacokinetics of ritonavir-boosted fosamprenavir during pregnancy and postpartum. Amprenavir (the active moiety of fosamprenavir) and ritonavir intensive pharmacokinetic evaluations were performed at steady state during the second and third trimesters of pregnancy and postpartum. Plasma concentrations of amprenavir and ritonavir were measured using high-performance liquid chromatography. The target amprenavir area under the concentration-versus-time curve (AUC) was higher than the 10th percentile (27.7 μg · h/ml) of the median area under the curve for ritonavir-boosted fosamprenavir in adults receiving twice-daily fosamprenavir-ritonavir at 700 mg/100 mg. Twenty-nine women were included in the analysis. The amprenavir AUC from time zero to 12 h (AUC0–12) was lower (geometric mean ratio [GMR], 0.60 [confidence interval {CI}, 0.49 to 0.72] [P < 0.001]) while its apparent oral clearance was higher (GMR, 1.68 [CI, 1.38 to 2.03] [P < 0.001]) in the third trimester than postpartum. Similarly, the ritonavir AUC0–12 was lower in the second (GMR, 0.51 [CI, 0.28 to 0.91] [P = 0.09]) and third (GMR, 0.72 [CI, 0.55 to 0.95] [P = 0.005]) trimesters than postpartum, while its apparent oral clearance was higher in the second (GMR, 1.98 [CI, 1.10 to 3.56] [P = 0.06]) and third (GMR, 1.38 [CI, 1.05 to 1.82] [P = 0.009]) trimesters than postpartum. The amprenavir area under the curve exceeded the target for 6/8 (75%) women in the 2nd trimester, 18/28 (64%) in the 3rd trimester, and 19/22 (86.4%) postpartum, and the trough concentrations (Cmin) of amprenavir were 4- to 16-fold above the mean amprenavir-protein-adjusted 50% inhibitory concentration (IC50) of 0.146 μg/ml. Although amprenavir plasma concentrations in women receiving ritonavir-boosted fosamprenavir were lower during pregnancy than postpartum, the reduced amprenavir concentrations were still above the exposures needed for viral suppression.
Lifestyle changes for the treatment of nonalcoholic fatty liver disease - A 2015-19 update.

BACKGROUND Lifestyle interventions aimed at weight loss have been associated with improved liver enzymes, reduced intrahepatic triglyceride content and improved histology (including reduced fibrosis stage). OBJECTIVE To revise the evidence on the beneficial effects of lifestyle changes accumulated since 2015, following the publication of the pivotal Cuban experience with histologic outcome. METHODS A PubMed search covering the period 2015 to July 2019 was carried out. All retrieved references were analyzed, and double checked by authors. RESULTS 20 new studies were identified; in addition, two relevant studies provided new evidence. Thirteen studies were classified as randomized, controlled studies, three as proof-of-concept/pilot studies, four as cohort observational studies. In an attempt to maintain a closer contact between participants and the treatment center, a study implemented regular phone calls, another an e-mail service, a third was based on text messages, and finally a study was totally web based. Notably, the web-based treatment, accessed following intense motivational interviewing, was not less effective than a standard group-based behavior program. CONCLUSION Lifestyle changes should form the basis of any NAFLD intervention. Information technology provides the opportunity to expand treatment, bypassing job and time constraints in younger patients, and to maintain long-term contact between patients and therapists in the NAFLD population.
Phylodynamic Analysis Complements Partner Services by Identifying Acute and Unreported HIV Transmission

Tailoring public health responses to growing HIV transmission clusters depends on accurately mapping the risk network through which it spreads and identifying acute infections that represent the leading edge of cluster growth. HIV transmission links, especially those involving persons with acute HIV infection (AHI), can be difficult to uncover, or confirm during partner services investigations. We integrated molecular, epidemiologic, serologic and behavioral data to infer and evaluate transmission linkages between participants of a prospective study of AHI conducted in North Carolina, New York City and San Francisco from 2011–2013. Among the 547 participants with newly diagnosed HIV with polymerase sequences, 465 sex partners were reported, of whom only 35 (7.5%) had HIV sequences. Among these 35 contacts, 23 (65.7%) links were genetically supported and 12 (34.3%) were not. Only five links were reported between participants with AHI but none were genetically supported. In contrast, phylodynamic inference identified 102 unreported transmission links, including 12 between persons with AHI. Importantly, all putative transmission links between persons with AHI were found among large clusters with more than five members. Taken together, the presence of putative links between acute participants who did not name each other as contacts that are found only among large clusters underscores the potential for unobserved or undiagnosed intermediaries. Phylodynamics identified many more links than partner services alone and, if routinely and rapidly integrated, can illuminate transmission patterns not readily captured by partner services investigations.
Protective effect of microRNA-381 against inflammatory damage of endothelial cells during coronary heart disease by targeting CXCR4

Coronary heart disease (CHD) is the leading cause of human morbidity and mortality worldwide. MicroRNA (miRNA) profiling is an innovative method of identifying biomarkers for many diseases and may be a powerful tool in the diagnosis and treatment of CHD. The present study aimed to analyze the effects of miRNA (miR)-381 on the inflammatory damage of endothelial cells during CHD. A total of 21 patients with CHD and 21 healthy control patients were enrolled in this study. Reverse transcription-quantitative PCR, western blotting and immunofluorescence assays were conducted to examine the expression levels of miR-381, C-X-C chemokine receptor type 4 (CXCR4), Bcl-2, Bax, Cleaved-Caspases-3 and −9, p38, ERK1/2 and JNK. Cell Counting Kit-8, EdU and flow cytometry experiments were performed to evaluate cell proliferation and apoptosis. An ELISA was adopted to determine the expressions of inflammatory factors (interleukins-8, −6 and −1β, and tumor necrosis factor-α). In addition, a dual-luciferase reporter assay was used to determine the relationship between miR-381 and CXCR4. Decreased miR-381 expression and increased CXCR4 expression in the plasma were observed in the CHD group compared with the normal group, which indicated a negative relationship between miR-381 and CXCR4. Overexpression of miR-381 significantly promoted the proliferation and inhibited the apoptosis of oxidized low-density lipoprotein (OX-LDL)-induced human umbilical vein endothelial cells (HUVECs) through mitogen-activated protein kinase pathway by targeting and inhibiting CXCR4. Furthermore, overexpression of miR-381 reduced the release of inflammatory factors in OX-LDL-induced HUVECs. By contrast, reduced expression of miR-381 exerted the opposite effects, which were subsequently reversed by silencing CXCR4 expression. Results from the present study indicated that miR-381 was a CHD-related factor that may serve as a potential molecular target for CHD treatment.
Screening for Small Molecule Modulators of Trypanosoma brucei Hsp70 Chaperone Activity Based upon Alcyonarian Coral-Derived Natural Products

The Trypanosoma brucei Hsp70/J-protein machinery plays an essential role in survival, differentiation, and pathogenesis of the protozoan parasite, and is an emerging target against African Trypanosomiasis. This study evaluated a set of small molecules, inspired by the malonganenones and nuttingins, as modulators of the chaperone activity of the cytosolic heat inducible T. brucei Hsp70 and constitutive TbHsp70.4 proteins. The compounds were assessed for cytotoxicity on both the bloodstream form of T. b. brucei parasites and a mammalian cell line. The compounds were then investigated for their modulatory effect on the aggregation suppression and ATPase activities of the TbHsp70 proteins. A structure–activity relationship for the malonganenone-class of alkaloids is proposed based upon these results.
A Pilot Study of Chicago Waterways as Reservoirs of Multidrug-Resistant Enterobacteriaceae (MDR-Ent) in a High-Risk Region for Community-Acquired MDR-Ent Infection in Children

Community-acquired multidrug resistant Enterobacteriaceae (MDR-Ent) infections continue to increase in the United States. In prior studies, we identified neighboring regions in Chicago, Illinois, where children have 5 to 6 times greater odds of MDR-Ent infections. To prevent community spread of MDR-Ent, we need to identify the MDR-Ent reservoirs. A pilot study of 4 Chicago waterways for MDR-Ent and associated antibiotic resistance genes (ARGs) was conducted. Three waterways (A1 to A3) are labeled safe for “incidental contact recreation” (e. ABSTRACT Community-acquired multidrug resistant Enterobacteriaceae (MDR-Ent) infections continue to increase in the United States. In prior studies, we identified neighboring regions in Chicago, Illinois, where children have 5 to 6 times greater odds of MDR-Ent infections. To prevent community spread of MDR-Ent, we need to identify the MDR-Ent reservoirs. A pilot study of 4 Chicago waterways for MDR-Ent and associated antibiotic resistance genes (ARGs) was conducted. Three waterways (A1 to A3) are labeled safe for “incidental contact recreation” (e.g., kayaking), and A4 is a nonrecreational waterway that carries nondisinfected water. Surface water samples were collected and processed for standard bacterial culture and shotgun metagenomic sequencing. Generally, A3 and A4 (neighboring waterways which are not hydraulically connected) were strikingly similar in bacterial taxa, ARG profiles, and abundances of corresponding clades and genera within the Enterobacteriaceae. Additionally, total ARG abundances recovered from the full microbial community were strongly correlated between A3 and A4 (R2 = 0.97). Escherichia coli numbers (per 100 ml water) were highest in A4 (783 most probable number [MPN]) and A3 (200 MPN) relative to A2 (84 MPN) and A1 (32 MPN). We found concerning ARGs in Enterobacteriaceae such as MCR-1 (colistin), Qnr and OqxA/B (quinolones), CTX-M, OXA and ACT/MIR (beta-lactams), and AAC (aminoglycosides). We found significant correlations in microbial community composition between nearby waterways that are not hydraulically connected, suggesting cross-seeding and the potential for mobility of ARGs. Enterobacteriaceae and ARG profiles support the hypothesized concerns that recreational waterways are a potential source of community-acquired MDR-Ent.
Coupled Methyl Group Rotation in FMN Radicals Revealed by Selective Deuterium Labeling.

Flavin semiquinones are common intermediate redox states in flavoproteins, and thus, knowledge of their electronic structure is essential for fully understanding their chemistry and chemical versatility. In this contribution, we use a combination of high-field ENDOR spectroscopy and selective deuterium labeling of flavin mononucleotide (FMN) with subsequent incorporation as cofactor into a variant Avena sativa LOV domain to extract missing traits of the electronic structure of a protein-bound FMN radical. From these experiments, precise values of small proton hyperfine and deuterium nuclear quadrupole couplings could be extracted. Specifically, isotropic hyperfine couplings of -3.34 MHz, -0.11 MHz and +0.91 MHz were obtained for the protons H(6), H(9) and H(7α), respectively. These values are discussed in the light of specific protein-cofactor interactions. Furthermore, the temperature behavior of the H(7α) methyl-group rotation elicited by its energy landscape was analyzed in greater detail. Pronounced interplay between the two methyl groups at C(7) and C(8) of FMN could be revealed. Most strikingly, this rotational behavior could be modulated by selective deuterium editing.
HO-1 induced autophagy protects against IL-1 β-mediated apoptosis in human nucleus pulposus cells by inhibiting NF-κB

In this study, we investigated the role of heme oxygenase-1 (HO-1) in intervertebral disc degeneration (IDD) by assessing the effects of HO-1 overexpression on IL-1β-induced apoptosis in nucleus pulposus cells (NPCs). Immunohistochemical staining showed HO-1 expression to be lower in NPCs from IDD patients than from patients with lumbar vertebral fractures (LVF). Western blot analysis showed HO-1 and LC3-II/I levels to be lower in NP tissues from IDD patients than from LVF patients, suggesting suppression of autophagy in degenerative intervertebral disc. Consistent with that idea, autophagy was increased in HO-1-overexpressing NPCs while IL-1β-induced apoptosis was reduced. These effects were reversed by treatment with the early autophagy inhibitor 3-methyl adenine, which suggests HO-1-induced autophagy suppresses IL-1β-induced apoptosis in NPCs. HO-1 overexpression promoted autophagy by increasing levels of Beclin-1/PI3KC3 complex. Phospho-P65 levels were lower in HO-1-overexpressing NPCs, suggesting inhibition of NF-κB-mediated apoptosis. Our study thus demonstrates that HO-1 promotes autophagy by enhancing formation of Beclin-1/PI3KC3 complex and suppresses IL-1β-induced apoptosis by inhibiting NF-κB. We suggest that HO-1 is a potential therapeutic target to alleviate IDD.
Thermoresponsive Inverted Colloidal Crystal Hydrogel Scaffolds for Lymphoid Tissue Engineering

Inverted colloidal crystal (ICC) hydrogel scaffolds represent unique opportunities in modeling lymphoid tissues and expanding hematopoietic‐lymphoid cells. Fully interconnected spherical pore arrays direct the formation of stromal networks and facilitate interactions between stroma and hematopoietic‐lymphoid cells. However, due to the intricate architecture of these materials, release of expanded cells is restricted and requires mechanical disruption or chemical dissolution of the hydrogel scaffold. One potent biomaterials strategy to release pore‐entrapped hematopoietic‐lymphoid cells without breaking the scaffolds apart is to transiently increase the dimensions of these materials using stimuli‐responsive polymers. Having this mindset, thermoresponsive ICC scaffolds that undergo rapid (<1 min) and substantial (>300%) diameter change over a physiological temperature range (4–37 °C) by using poly(N‐isopropylacrylamide) (PNIPAM) with nanogel crosslinkers is developed. For a proof‐of‐concept study, the stromal niche by creating osteospheroids, aggregates of osteoblasts, and bone chips is first replicated, and subsequently Nalm‐6 model hematopoietic‐lymphoid cells are introduced. A sixfold increase in cell count is harvested when ICC hydrogel scaffolds are expanded without termination of the established 3D stromal cell culture. It is envisioned that thermoresponsive ICC hydrogel scaffolds will enable for scalable and sustainable ex vivo expansion of hematopoietic‐lymphoid cells.