Miracle-dz/UniFAR-FTUs huggingface dataset:
Release of polychlorinated biphenyl congeners in a contaminated harbor and canal

The overall hypothesis of this thesis addresses the release of polychlorinated biphenyls (PCBs) in the sediments of a highly contaminated harbor. I collected, analyzed and quantified PCB congeners in more than 130 samples of air, water and sediment. Then I constructed a chemical fate model as function of chemical concentrations, physicalchemical properties, local meteorological and hydraulic conditions. Indiana Harbor and Ship Canal in East Chicago (IHSC), Indiana, was selected for its expected high levels of PCBs in the sediment and because of future plans for dredging. I found that PCB concentrations in air, water and sediment in this area were much higher than background levels in the Great Lakes region. PCB sediment concentrations were above the threshold limit to designate IHSC as a Superfund site (≥ 50 ppm), although it is not. The PCB signature in surficial sediment strongly resembles the original Aroclor 1248 but deeper layers show evidence of mixtures of Aroclors and weathering processes. The fate model showed that IHSC contaminated sediments are a continuous source of PCBs to the water and overlying air, and also produce a PCB input to Lake Michigan, even under quiescent conditions. The PCB signature in sediment, water, and air support my determination that the contaminated sediment is a major source of PCBs into the water and air above it. Simulations considering different surficial sediment concentrations post-dredging demonstrated that PCB concentrations in the sediment should be considered in the dredging operation to minimize the release of PCBs into the environment. Finally, I examined the role of the dissolved sediment porewater concentration in the prediction of sediment-water soluble fluxes, using a passive sampler technique (SPME PDMS-fiber) and calculated values from a one-parameter linear free energy relationship (op-LFER). I determined that the latter overestimates the freely dissolved porewater concentration but are nevertheless the most appropriate values for predicting PCBs soluble release from contaminated sediments.
Evaluation of the Impact of a Low Back Pain Educational Intervention on Physicians’ Practice Patterns and Patients’ Outcomes

This study was designed to evaluate the effects of an educational intervention on physicians’ management of low back pain patients. The study universe composed of 64 providers employed by a large occupational health group, with 4411 LBP cases pretraining and 4665 cases posttraining selected from the organization’s database. The control group had 151 providers with 8478 pretraining and 8876 posttraining cases. Results showed that practices of physicians who participated in the intervention strategy underwent significant changes between the two intervals. Specifically, the intervention group reduced the percentage of restricted work cases, reduced the percentage of lost-time cases for male patients and female patients (less than 40 years old), and shortened restricted workday duration and total case duration for female patients. These results provide early indication for the effectiveness of this type of educational intervention strategy.
Funding liquidity risk and financial stability: evidence from cooperative banks

In 2010 the Basel Committee on Banking Supervision (BCBS) introduced new liquidity rules phased in under Basel III and, specifically, defined the Net Stable Funding Ratio (NSFR) with the aim of making the financial system more stable and resilient. The aim of this analysis is to examine the relationship between the NSFR and banks’ stability with a particular focus on cooperative industry. Based on a panel dataset of 1,173 cooperative banks from Austria, Germany and Italy, observed over the years 2011-2018, I find that stability improves for cooperative banks that have higher NSFRs, but there is a point at which increasing further the NSFR diminishes their stability. The marginal impact of the NSFR on cooperative banks’ stability increases as the banks efficiency increases, and diminishes as the income diversification and the size increase. Results remain robust after some robustness tests.
Ground-Based Observations of Terrestrial Gamma Ray Flashes Associated with Downward-Directed Lightning Leaders

Terrestrial gamma-ray flashes (TGFs) are bursts of gamma-rays initiated in the Earth’s atmosphere. TGFs were serendipitously first observed over twenty years ago by the BATSE gamma ray satellite experiment. Since then, several satellite experiments have shown that TGFs are produced in the upward negative breakdown stage at the start of intracloud lightning discharges. In this proceeding, we present ground-based observation of TGFs produced by downward negative breakdown occurring at the beginning of negative cloud-to-ground flashes. The Terrestrial gamma-ray flashes discussed in this work were detected between 2014-2017 at ground level by the Telescope Array surface detector (TASD) together with Lightning Mapping Array (LMA) and the slow electric field antenna (SA). The TASD detector is a 700 km2 ultra high energy cosmic ray detector in the southwestern desert of Utah. It is comprised of 507 (3 m2) plastic scintillator detectors on a 1.2 km square grid. The LMA detector, a three-dimensional total lightning location system, is comprised of nine stations located within and around the array. The slow electric field antenna records the electric field change in lightning discharges. The observed Gamma ray showers were detected in the first 1-2 ms of downward negative breakdown prior to cloud-to-ground lightning strikes. The shower sources were observed by the LMA detector at altitudes of a few kilometers above ground level. The detected energetic burst showers have a footprint on the ground typically ~ 3-5 km in diameter. The bursts comprise of several (2-5) individual pulses, each of which have a span of a few to tens of microseconds and an overall duration of several hundred microseconds. Using a forward-beamed cone of half-angle of 16 degrees, GEANT simulation studies indicate that the showers are consistent with gamma rays of 1012 - 1014 primary photons. We hypothesize that the observed terrestrial gamma-ray flashes are similar to those detected by satellites, but that the ground-based observations are closer to the source and therefore are able to observe weaker sources and report on the structure of the temporal distribution at the source. This result and future studies will enable us to better identify and constrain the mechanisms of downward TGF production.
Effect of Pine Needle Mulch and Irrigation Frequency on the Yield of Origanum syriacum under Open Field Condition

Due to the intensive harvest from natural habitat and increasing competition as a source of food, O. syriacum was introduced into cultivation and soon became one of the promising crops for many farmers in rural areas. The aim of the study is to investigate the effect of pine needle mulch(PN) and irrigation frequency(IF) at 5, 10 and 15 days on the yield under open field conditions. The study was conducted at the Lebanese agricultural research institute (LARI) in Lebaa station (33°32.681′ North, 35°27.088′ East, 354 m a.s.l.), south Lebanon, province of Jizzin, under open field condition for two seasons during 2016. Treatments were organized in randomized complete block design (RCBD) with three replicates. The results indicated a significant effect of mulch in both spring and fall seasons F (1, 172) = 59.34, p < . 0001, η²=. 24, F (1, 172) = 77.71, p < . 0001, η²=. 30 respectively. The two-way anova showed no significant effect of irrigation frequency on the average and total plant fresh weight (PFW) across two seasons F (2, 349) = . 80, p= . 4522, η²=. 0038, F (2, 159) = 1.07, p= . 3460, η²=. 007 respectively. Very little variance of the plant fresh weight ,(0.2% – spring and 3.1 %- fall) was attributed to the interaction of mulch and irrigation frequency . In a comparison between percent weight contribution(PWC) of a different plant part, leaves formed the highest proportion (48.6%) compared to the inflorescence and stem. The fresh weight of weeds(g/ m2 ) was significantly less in plots mulched with pine needles compared to the control (F(1,66)=24.43, p<. 0001, η²=. 75). Applying pine needle mulch enhanced most of the yield parameters. Under calcareous clayey soil O. syriacum could be irrigated at10 or 15 days frequencies without remarkable decrease in the yield.
Determinants of Undernutrition Among Adult People on Antiretroviral Therapy in Goba Hospital, Southeast Ethiopia: A Case–Control Study

Background: Nutritional status affects effectiveness and adherence to antiretroviral therapy, survival status, and quality-of-life in people living with human immunodeficiency virus. Prevalence of undernutrition among HIV infected people in Ethiopia ranges from 12.3% to 55.6%. Objective: To identify determinants of undernutrition among adult people on antiretroviral therapy in Goba Hospital, Southeast Ethiopia. Methods: A facility-based case–control study was conducted on 276 study participants from March 16 to May 26, 2019. Nutritional status was determined by body mass index (BMI), where BMI<18.5 kg/m 2 was defined as malnutrition. A pretested structured questionnaire was used to collect data by face-to-face interview. Data were entered into Epi-data version 4.4 and then exported to SPSS version 23 for analyses. Bivariable and multiple binary logistic regression were fitted. Multicollinearity was checked among candidate variables using variance inflation factor. P -value<0.05 was considered statistically significant and AORs at 95% CIs was used to assess the strength of association. Results: The response rate of participants was 97% among cases and 95% among controls. Nearly two-thirds (65%) of cases and 54.3% of controls were females. Factors significantly associated with undernutrition were household food insecurity (AOR=3.24, 95% CI=1.72– 6.08), depression (AOR=2.07, 95% CI=1.16–3.72), current alcohol consumption (AOR=3.80, 95% CI=1.71–8.43), and non-adherence to antiretroviral therapy (AOR=2.61, 95% CI=1.28–5.30). Conclusion: Household food insecurity, depression, current alcohol consumption, and non-adherence to ART were associated with undernutrition. Strengthening the strategies and programs that target food assistance besides therapeutic interventions, addressing problems related to adherence of ART, incorporating psychosocial information about depression and substance use during counseling provided by healthcare providers for PLHIV and further longitudinal study were recommended.
The Plasma Proteome Identifies Expected and Novel Proteins Correlated with Micronutrient Status in Undernourished Nepalese Children 1 – 3

Micronutrient deficiencies are common in undernourished societies yet remain inadequately assessed due to the complexity and costs of existing assays. A plasma proteomics-based approach holds promise in quantifying multiple nutrient:protein associations that reflect biological function and nutritional status. To validate this concept, in plasma samples of a cohort of 500 6to 8-y-old Nepalese children, we estimated cross-sectional correlations between vitamins A (retinol), D (25-hydroxyvitamin D), and E (a-tocopherol), copper, and selenium, measured by conventional assays, and relative abundance of their major plasmabound proteins, measured by quantitative proteomics using 8-plex iTRAQ mass tags. The prevalence of low-to-deficient status was 8.8% (<0.70 mmol/L) for retinol, 19.2% (<50 nmol/L) for 25-hydroxyvitamin D, 17.6% (<9.3 mmol/L) for a-tocopherol, 0% (<10 mmol/L) for copper, and 13.6% (<0.6 mmol/L) for selenium. We identified 4705 proteins, 982 in >50 children. Employing a linear mixed effects model, we observed the following correlations: retinol:retinol-binding protein 4 (r = 0.88), 25-hydroxyvitamin D:vitamin D-binding protein (r = 0.58), a-tocopherol:apolipoprotein C-III (r = 0.64), copper:ceruloplasmin (r = 0.65), and selenium: selenoprotein P isoform 1 (r = 0.79) (all P < 0.0001), passing a false discovery rate threshold of 1% (based on P value-derived q values). Individual proteins explained 34–77% (R) of variation in their respective nutrient concentration. Adding second proteins tomodels raisedR to 48–79%, demonstrating a potential to explain additional variation in nutrient concentration by this strategy. Plasma proteomics can identify and quantify protein biomarkers ofmicronutrient status in undernourished children. The maternalmicronutrient supplementation trial, fromwhich datawere derived as a follow-up activity,was registered at clinicaltrials. gov as NCT00115271. J. Nutr. 143: 1540–1548, 2013.
3D SPARKLING trajectories for high-resolution T2*-weighted Magnetic Resonance imaging

—We have recently proposed a new optimization algorithm called SPARKLING (Spreading Projection Algorithm for Rapid K-space sampLING) to design efﬁcient Compressive Sampling patterns for Magnetic Resonance Imaging. This method has a few advantages over standard trajectories such as radial lines or spirals: i) it allows to sample the k-space along any arbitrary density while the other two are restricted to radial densities and ii) it achieves a higher image quality for a given readout time. Here, we introduce an extension of the SPARKLING method for 3D imaging that allows to achieve an isotropic resolution of 600 µ m in just 45 seconds, compared to a scan duration of 14 min 31 s using 4-fold accelerated parallel imaging, for T2*-weighted ex vivo brain imaging at 7 Tesla over a ﬁeld-of-view of 200 × 200 × 140 mm 3 .
The prepared sample libraries were quantified by qPCR using KAPA Biosystem ’ s next-generation sequencing library qPCR kit and run on a Roche LightCycler

1 Washington State University Tri-Cities, Richland, WA, USA 2 Argonne National Laboratory, Lemont, IL, USA 3 Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, CA, USA 4 DOE Joint Genome Institute, Walnut Creek, CA, USA 5 Lawrence Berkeley National Laboratory, Berkeley, CA, USA 6 University of Chicago, Chicago, IL, USA 7 USGS, Menlo Park, CA, USA 8 Washington State University, Pullman, WA, USA 9 Pacific Northwest National Laboratory, Chemical & Biolog ical Process Development Group, Richland, WA, USA 10 Environmental Molecular Sciences Laboratory, Richland, WA, USA
Assessment of Bacterial Profile of Ocular Infections among Subjects Undergoing Ivermectin Therapy in Onchocerciasis Endemic Area in Nigeria

Bacteria are the major contributor of ocular infections worldwide. This can damage the structures of the eye with possible blindness and visual impairments, if left untreated. This study was undertaken to determine bacterial agents of conjunctivitis among individuals from onchocerciasis endemic area in Anambra State, Nigeria. This was a cross-sectional study involving ninety-two (92) randomly recruited test subjects undergoing ivermectin therapy aged between 11-80 years with signs and symptoms of onchocerciasis infection and bacterial conjunctivitis at Isu-Anaocha community in Anambra state between October and November, 2016. Ninety-two (92) apparently healthy subjects without signs and symptoms of onchocerciasis and bacterial conjunctivitis with normal vision, within the age of 11-80 years from the same community were used as control subjects, making a total of 184 participants. Visual acuity test was conducted on the participants using Snellen’s alphabet chart and illiterate E chart. Phenotypic and antibiotic susceptibility tests of these isolates were carried out according to Kirby - Bauer disc diffusion method guidelines. In the test group, 22 out of 92 conjunctival samples yielded bacterial growth, giving percentage prevalence of 23.9%, with age group 41-50 years having the highest frequency 7(31.8%) among individuals co-infected with onchocerciasis infection whereas 72 out of 92 conjunctival samples in the control group yielded bacterial growth giving percentage prevalence of 78.3%, with age group 41-50 years having the highest frequency 35(37.2%) among individuals that had no signs and symptoms of onchocerciasis infection. The predominant bacteria isolated was Staphylococcus aureus 8(36%) in the test group and 20 (28%) in the control group, giving a total of 28 (30%). Other bacterial isolates were Streptococcus pneumoniae 17 (18%), Staph. epidermidis 15 (16%), Escherichia coli 13(14%), Pseudomonas aeruginosa 12(13%) and Salmonella spp. 9(9%). Antibiotic susceptibility testing showed that Gentamicin and fluoroquinolones are most active against Gram positive bacteria in conjunctivitis while Augmentin was found to be the most active against Gram negative organisms, therefore, recommended as first line drug. Visual acuity (VA) test done on the test group showed that 52 (57%) persons had normal vision, 20 (22%) had mild visual impairment, 15 (16%) had moderate visual impairment, 5(5%) had severe visual impairment but none was blind. All forms of visual impairment are not wholly attributable to bacterial conjunctivitis as some could be due to ageing and uncorrected refractive errors.
Rotavirus vaccines

Two live attenuated oral rotavirus vaccines were licensed in 2006 for prevention of severe acute gastroenteritis in children: Rotarix™ (GSK), a human rotavirus vaccine with G1P[8] serotype characteristics and RotaTeq™ (Merck), a bovine-human reassortant vaccine expressing human G 1–4 and P[8] antigens. In prelicensure trials both vaccines showed high efficacy against severe RV gastroenteritis, low reactogenicity and no increased risk for intussusception (IS) (Ruíz-Palacios et al., 2006; Vesikari et al., 2006). Both vaccines have now been distributed in millions of doses. Post-marketing data have not shown any gross signal for IS with either vaccine, but further data and analyses are required for final conclusion on safety of these vaccines.
How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model (TRiPS)

The fossil record is a rich source of information about biological diversity in the past. However, the fossil record is not only incomplete but has inherent biases due to geological, physical, chemical and biological factors. Our knowledge of past life is also biased because of differences in academic and amateur interests and sampling efforts. As a result, not all individuals or species that lived in the past are equally likely to be discovered at any point in time or space. To reconstruct temporal dynamics of diversity using the fossil record, biased sampling must be explicitly taken into account. Here, we introduce an approach that utilizes the variation in the number of times each species is observed in the fossil record to estimate both sampling bias and true richness. We term our technique TRiPS (True Richness estimated using a Poisson Sampling model) and explore its robustness to violation of its assumptions via simulations. We then venture to estimate sampling bias and absolute species richness of dinosaurs in the geological stages of the Mesozoic. Using TRiPS, we estimate that 1936 (1543-2468) species of dinosaurs roamed the Earth during the Mesozoic. We also present improved estimates of species richness trajectories of the three major dinosaur clades; the sauropodomorphs, ornithischians and theropods, casting doubt on the Jurassic-Cretaceous extinction event and demonstrating that all dinosaur groups are subject to considerable sampling bias throughout the Mesozoic.
How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model (TRiPS)

14 The fossil record is a rich source of information about biological diversity in the past. However, the fossil 15 record is not only incomplete but has inherent biases due to geological, physical, chemical and biological 16 factors. Our knowledge of past life is also biased because of differences in academic and amateur interests 17 and sampling efforts. As a result, not all individuals or species that lived in the past are equally likely to 18 be discovered at any point in time or space. To reconstruct temporal dynamics of diversity using the fossil 19 record, biased sampling must be explicitly taken into account. Here, we introduce an approach that 20 utilizes the variation in the number of times each species is observed in the fossil record to estimate both 21 sampling bias and true richness. We term our technique TRiPS (True Richness estimated using a Poisson 22 Sampling model) and explore its robustness to violation of its assumptions via simulations. We then 23 venture to estimate sampling bias and absolute species richness of dinosaurs in the geological stages of 24 the Mesozoic. Using TRiPS, we estimate that 1936 (1543-2468) species of dinosaurs roamed the Earth 25 during the Mesozoic. We also present improved estimates of species richness trajectories of the three 26 major dinosaur clades; the sauropodomorphs, ornithischians and theropods, casting doubt on the Jurassic- 27 Cretaceous extinction event and demonstrating that all dinosaur groups are subject to considerable 28 sampling bias throughout the Mesozoic. 30 31 32
Maintenance of epidermal architecture by CLASP2 and p120-catenin

Adherens Junctions are cadherin-based structures fundamental for the maintenance of cell-cell adhesion, and thus preservation of proper tissue architecture and function. To do so, they establish connections with the cytoskeleton, both with actin filaments and microtubules, enabling cells to respond to injury and external stimuli as a coordinated tissue. Previous findings have illustrated connections between cadherins and microtubule minus- and plus-ends. However, the functional relevance of such interactions and the molecular players are still under debate. Moreover, the involvement of these particular connections in the homeostasis of specific tissues remains unexplored. In this thesis project we investigated how microtubules reach Adherens Junctions in basal cells of the epidermis. We identified a novel interaction between the microtubule plus-end binding protein CLASP2 and the cadherin binding molecule p120 at Adherens Junctions. In the absence of CLASP2, Adherens Junctions do not form properly and present altered dynamics, which leads to a disruption of cell-cell adhesion. This phenotype is accompanied by alterations in microtubule dynamics at Adherens Junctions, in terms of speed and directionality. The same alterations are observed in the absence of p120, suggesting that the CLASP2-p120 interaction contributes to microtubule targeting to Adherens Junctions. Importantly, since CLASP2 expression is enriched in basal progenitor cells of the epidermis, the CLASP2-p120 interaction seems to be restricted to this specific epidermal compartment, where it may dynamically regulate cell-cell adhesion. On the contrary, the microtubule minus-end binding protein Nezha localizes to cell-cell contacts in suprabasal differentiated keratinocytes. Loss of CLASP2 leads to alterations in the proliferation-differentiation balance of basal keratinocytes. This alteration could be the result of weakened Adherens Junctions but it may also reflect a defect in the correct orientation of the spindle via interaction with p120. Overall, the work presented in this doctoral thesis supports a model where microtubule plus-ends are targeted to Adherens Junctions in basal keratinocytes via the CLASP2-p120 interaction whereas minus-ends are captured at cell-cell adhesion sites in differentiated cells. This could be an important mechanism to control Adherens Junction stability and dynamics in epidermal progenitor cells.