Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of Salmonella in animal food

Salmonella contamination in animal food production facilities is a growing concern. The bacteria has been the cause of 40% of pet food recalls in the past 5 years, and there are potential human health implications because pet food is a direct human contact food. A potential method to reduce Salmonella contamination in pet food is through the use of acidifiers and desiccants to destroy and inhibit growth of bacteria. The objective of this thesis was to quantify Salmonella contamination in livestock feed and pet food manufacturing facilities, and propose mitigation measures to mitigate the presence of pathogens in animal food. Therefore, the objective of Experiment 1 was to investigate sources of Salmonella contamination throughout livestock feed (n = 2) and pet food (n = 2) manufacturing facilities on a specific sampling day. Salmonella was present in all four facilities. However, one of the livestock feed manufacturing facilities had more than double the Salmonella-positive locations than all other facilities. This experiment demonstrated that surface type and location should be taken into consideration when controlling Salmonella contamination. In Experiments 2 and 3, the use of a commercial powdered dry acidulant, sodium bisulfate, was studied as a coating of dog kibble to reduce and prevent Salmonella growth over time. The coating reduced Salmonella concentration, and its efficacy was not impacted by altering the bulk density or surface area of the kibble. Experiment 4 was conducted to determine the efficacy of sodium bisulfate added to poultry mash to reduce or prevent Salmonella growth over time. The inclusion of the dry acidulant did not reduce Salmonella concentration; however, storage time reduced Salmonella contamination in poultry feed. In summary, Salmonella contamination exists in manufacturing facilities, but the location and magnitude of contamination differs. Furthermore, sodium bisulfate effectively reduces Salmonella contamination when applied as a pet food coating, but not in poultry feed.
The State of the Oligocene Icehouse World: Sedimentology, Provenance, and Stable Isotopes of Marine Sediments from the Antarctic Continental Margin

Ice-rafted debris concentrations and Ar/Ar thermochronology from Integrated Ocean Drilling Program (IODP) Site U1356 reveal an ice sheet was consistently present in the Wilkes subglacial basin (WSB) and Adélie regions of Antarctica during the Late Oligocene, even though atmospheric CO2 levels were elevated. According to climate modeling, the WSB is one of the most sensitive regions of East Antarctica and is thought to be the first regions that experiences ice sheet retreat during warming. Concentrations of ice-rafted debris suggest iceberg delivery to Site U1356 is paced by 405-kry eccentricity cycles, with IRD being delivered to the drill site during cooler times. A comparison with ice-volume estimates suggests IRD are delivered to Site U1356 when ice volume is at least 80 % of modern. The lack of IRD during warmer periods suggests a retreat of the ice sheet from the coastline or a change in oceanographic conditions that prevent many icebergs from reaching Site U1356. Debris flow layers have a good correlation with oxygen isotope maxima and have been interpreted to represent an ice sheet larger than modern. The primary provenance of the IRD is from the Mertz Shear Zone region, which separates the Adélie craton from the WSB. Ages indicative of the Ross Orogeny comprise a secondary population that has been interpreted as being sourced from the Ninnis glacier or outlet glaciers further east. Additionally Grenville age grains comprise another population that can only be explained as being sourced from areas further inland that are currently obscured by the ice sheet. Together the concentrations and Ar/Ar provenance of the IRD show a large ice sheet
Palynology of the Cretaceous-Tertiary boundary in central Montana: Evidence for extraterrestrial impact as a cause of the terminal Cretaceous extinctions

This report details a statistical analysis of palynological change across iridium-enriched claystones defining the Cretaceous-Tertiary (K-T) boundary in the Cretaceous Hell Creek Formation and Tertiary Tullock Member of the Fort Union Formation, eastern Montana, United States. The results strongly support the bolide impact model of terminal Cretaceous extinctions. Chi-square analysis of presence and abundance below and above the iridium datum was used to define characteristic Cretaceous and Tertiary palynomorph species. There is no statistical support for gradual decline in Cretaceous species below the iridium datum, although the presence and abundance of certain Cretaceous species decline somewhat, and the presence of Tertiary species increases slightly, 0-3 m below the iridium datum. An estimated 15%-30% of the Hell Creek palynoflora disappear 0-2 cm above the iridium datum, and another 20%-30% undergoes a significant decline in abundance. Palynoflorules directly overlying the iridium datum are characteristically depauperate. Partial recovery of the palynoflora occurs within 10-20 cm of the boundary, but species richness remains depressed throughout the lower Tullock Member compared to the Hell Creek Formation. Palynoflorules from rare Hell Creek coals contain significantly fewer Cretaceous and significantly more Tertiary species, relative to those of flood-plain deposits, suggesting that perhaps 30%-40% of affected Hell Creek species disappear or decline due to facies change. Greenhouse warming from impact-generated atmospheric CO 2 and consequent increased soil water saturation, combined with still uncertain mass-kill mechanisms, best fit the available data to explain the pattern of change in vegetation at the K-T boundary throughout the Western Interior.
Potential vorticity regimes over East Asia during winter

Nine potential vorticity (PV) regimes over East Asia are identified by applying a Self‐Organizing Map and Hierarchical Ascendant Classification regime analysis to the daily PV reanalysis fields on the 300 K isentropic surface for December–March 1948–2014. According to the surface temperature anomalies over East Asia, these nine regimes are further classified into three classes, i.e., cold class (three regimes), warm class (four regimes), and neutral class (two regimes). The PV‐based East Asian winter monsoon index (EAWMI) is used to study the relationship between PV distributions and the temperature anomalies. The magnitude of cold (warm) anomalies over the land areas of East Asia increases (decreases) quasi‐linearly with the EAWMI. Regression analysis reveals that cold temperature anomalies preferentially occur when the EAWMI exceeds a threshold at ∼0.2 PVU (where 1 PVU ≡ 10−6 m2 K kg−1 s−1). PV inversion uncovers the mechanisms behind the relationships between the PV regimes and surface temperature anomalies and reveals that cold (warm) PV regimes are associated with significant warming (cooling) in the upper troposphere and lower stratosphere. On average, cold regimes have longer durations than warm regimes. Interclass transition probabilities are much higher for paths from warm/neutral regimes to cold regimes than for paths from cold regimes to warm/neutral regimes. Besides, intraclass transitions are rare within the warm or neutral regimes. The PV regime analysis provides insight into the causes of severe cold spells over East Asia, with blocking circulation patterns identified as the primary factor in initiating and maintaining these cold spells.
Distributed Subgradient Method With Random Quantization and Flexible Weights: Convergence Analysis

The distributed subgradient (DSG) method is a widely used algorithm for coping with large-scale distributed optimization problems in machine-learning applications. Most existing works on DSG focus on ideal communication between cooperative agents, where the shared information between agents is exact and perfect. This assumption, however, can lead to potential privacy concerns and is not feasible when wireless transmission links are of poor quality. To meet this challenge, a common approach is to quantize the data locally before transmission, which avoids exposure of raw data and significantly reduces the size of the data. Compared with perfect data, quantization poses fundamental challenges to maintaining data accuracy, which further impacts the convergence of the algorithms. To overcome this problem, we propose a DSG method with random quantization and flexible weights and provide comprehensive results on the convergence of the algorithm for (strongly/weakly) convex objective functions. We also derive the upper bounds on the convergence rates in terms of the quantization error, the distortion, the step sizes, and the number of network agents. Our analysis extends the existing results, for which special cases of step sizes and convex objective functions are considered, to general conclusions on weakly convex cases. Numerical simulations are conducted in convex and weakly convex settings to support our theoretical results.
Outcomes in patients with sarcoidosis and COVID-19

Background and aim: The effect of COVID-19 in patients with sarcoidosis has not been fully explored. The aim was to conduct a retrospective cohort study investigating outcomes in patients with sarcoidosis who were hospitalized with COVID-19. Methods: We included patients who had diagnoses of sarcoidosis and COVID-19 between January 1, 2020, and February 28, 2021. Primary outcomes included development of critical COVID-19; need for supplemental oxygen, noninvasive ventilation, and invasive ventilation; and death. Association of comorbidities and immunosuppression therapy with outcomes were analyzed. Multiple logistic regression analysis was used to assess risk factors associated with critical COVID-19. Results: Of 1198 patients with COVID-19, 169 had sarcoidosis (14.1%) and 1029 (85.9%) did not (control group). Of the 169 patients with sarcoidosis and COVID-19, 84 (49.7%) were hospitalized (study group: mean age 62.4 years; 61.9% women; and 56.0% Black). The study group required supplemental oxygen (81% vs 62%; p = 0.001) and noninvasive ventilation (33.3% vs 6.4%; p < 0.001) more often and had lower mortality (15.5% vs. 30.4%; p = 0.004) than the control group. In patients hospitalized with COVID-19, sarcoidosis was not associated with critical COVID-19 (odds ratio, 0.77; 95% CI, 0.46-1.29; p = 0.317), but having sarcoidosis while taking immunosuppression therapy was associated with decreased risk of critical COVID-19 (odds ratio, 0.45; 95% CI, 0.31-0.65; p < 0.001). Conclusions: Patients with sarcoidosis may not be at increased risk of critical illness or death from COVID-19, and immunosuppression therapy in these patients may reduce the risk of critical COVID-19.
Homologous acetone carboxylases select Fe(II) or Mn(II) as the catalytic cofactor

ABSTRACT Acetone carboxylases (ACs) catalyze the metal- and ATP-dependent conversion of acetone and bicarbonate to form acetoacetate. Interestingly, two homologous ACs that have been biochemically characterized have been reported to have different metal complements, implicating different metal dependencies in catalysis. ACs from proteobacteria Xanthobacter autotrophicus and Aromatoleum aromaticum share 68% sequence identity but have been proposed to have different catalytic metals. In this work, the two ACs were expressed under the same conditions in Escherichia coli and were subjected to parallel chelation and reconstitution experiments with Mn(II) or Fe(II). Electron paramagnetic and Mössbauer spectroscopies identified signatures, respectively, of Mn(II) or Fe(II) bound at the active site. These experiments showed that the respective ACs, without the assistance of chaperones, second metal sites, or post-translational modifications facilitate correct metal incorporation, and despite the expected thermodynamic preference for Fe(II), each preferred a distinct metal. Catalysis was likewise associated uniquely with the cognate metal, though either could potentially serve the proposed Lewis acidic role. Subtle differences in the protein structure are implicated in serving as a selectivity filter for Mn(II) or Fe(II). IMPORTANCE The Irving-Williams series refers to the predicted stabilities of transition metal complexes where the observed general stability for divalent first-row transition metal complexes increase across the row. Acetone carboxylases (ACs) use a coordinated divalent metal at their active site in the catalytic conversion of bicarbonate and acetone to form acetoacetate. Highly homologous ACs discriminate among different divalent metals at their active sites such that variations of the enzyme prefer Mn(II) over Fe(II), defying Irving-Williams-predicted behavior. Defining the determinants that promote metal discrimination within the first-row transition metals is of broad fundamental importance in understanding metal-mediated catalysis and metal catalyst design. The Irving-Williams series refers to the predicted stabilities of transition metal complexes where the observed general stability for divalent first-row transition metal complexes increase across the row. Acetone carboxylases (ACs) use a coordinated divalent metal at their active site in the catalytic conversion of bicarbonate and acetone to form acetoacetate. Highly homologous ACs discriminate among different divalent metals at their active sites such that variations of the enzyme prefer Mn(II) over Fe(II), defying Irving-Williams-predicted behavior. Defining the determinants that promote metal discrimination within the first-row transition metals is of broad fundamental importance in understanding metal-mediated catalysis and metal catalyst design.
Large-scale Ecotourism – A Contradiction in Itself?

In a large number of attempts to define ecotourism researchers often suggest that one vital aspect of ecotourism is the scale of the operations. Ecotourism, so the argument goes, should be small-scale tourism. This view is often illustrated with a number of negative impacts of mass tourism on the environment and on the host communites. However, this paper introduces the reader to two major players in mass tourism, Europe's largest package tour operator TUI and Germany's secondlargest charter carrier LTU. Both are certainly not ecotour operations; however, both implemented a variety of policies and actions, which attempt to keep the environmental and social impacts in the destinations as low as possible. The examples show that positive action can be taken without compromising company operations and customer comfort.
Macrobenthos in Relation to Sediment Characteristics of NearshoreWaters of Chitrapur,West Coast of India Receiving Industrial Effluents

Spatial and temporal variations of macrobenthos in relation to sediment characteristics in the coastal waters of Chitrapur, west coast of India receiving industrial effluents was investigated during pre and post-monsoon seasons of the year 1997-1998. The quality composition of macorbenthos revealed the presence of six families of polychaetes, 16 families of molluscs and three families of echinoderms. Among the above three groups, molluscans formed the bulk of the benthos. Textural analyzes of sediment have shown the dominance of sand in nearshore stations, while at deeper stations, it was dominated by silty fraction. Changes in the textural characteristics of the sediment and the higher level of organic carbon were found to be associated with the reduced frequency of occurrence and abundance of macrobenthos at the stations located near the effluent outfall along 8 m depth contour of Chitrapur section.
Chronic intermittent ethanol exposure-induced m6A modifications around mRNA stop codons of opioid receptor genes

ABSTRACT Chronic alcohol consumption may alter mRNA methylation and expression levels of genes related to addiction and reward in the brain, potentially contributing to alcohol tolerance and dependence. Neuron-like (SH-SY5Y) and non-neuronal (SW620) cells were utilized as models to examine chronic intermittent ethanol (CIE) exposure-induced global m6A RNA methylation changes, as well as m6A mRNA methylation changes around the stop codon of three opioid receptor genes (OPRM1, OPRD1, and OPRK1), which are known to regulate pain, reward, and addiction behaviours. CIE exposure for three weeks significantly increased global RNA methylation levels in both SH-SY5Y (t = 3.98, P = 0.007) and SW620 (t = 2.24, P = 0.067) cells. However, a 3-week CIE exposure resulted in hypomethylation around mRNA stop codon regions of OPRM1 and OPRD1 in both cell lines [OPRM1(SH-SY5Y): t = -5.05, P = 0.0005; OPRM1(SW620): t = -3.19, P = 0.013; OPRD1(SH-SY5Y): t = -13.43, P < 0.00001; OPRD1(SW620): t = -4.00, P = 0.003]. Additionally, mRNA expression levels of OPRM1, OPRD1, and OPRK1 were downregulated (corresponding to mRNA hypomethylation) in both SH-SY5Y and SW620 cells after a 3-week CIE exposure. The present study demonstrated that chronic ethanol exposure altered global RNA methylation levels, as well as mRNA methylation and expression levels of opioid receptor genes in both neuron-like and non-neuronal cells. Our findings suggest a potential epitranscriptomic mechanism by which chronic alcohol consumption remodels the expression of reward-related and alcohol responsive genes in the brain, thus increasing the risk of alcohol use disorder development. Abbreviations: OPRM1: the μ-opioid receptor; OPRD1: the δ-opioid receptor; OPRK1: the κ-opioid receptor; CIE: chronic intermittent ethanol exposure; CIE+WD: chronic intermittent ethanol exposure followed by a 24-hr withdrawal; SH-SY5Y: human neuroblastoma cell Line; SW620: human colon carcinoma cell line; RT-qPCR: reverse transcription followed by quantitative polymerase reaction; MazF-RT-qPCR: MazF digestion followed by RT-qPCR
Statistical analysis of spatial and temporal variations in atmospheric electric fields from a regional array of field mills

Electric fields and currents of the global electric circuit have been measured at different locations and time periods around the globe, but a long‐term analysis from a regional array of electric field mills has never been performed. Kennedy Space Center (KSC) in Florida has an array of over 30 electric field mills that have been continuously operating and archiving data for over 18 years. KSC is also instrumented with many meteorological towers. With this initial statistical analysis of a long‐term data set four unique observations are reported that encompass global as well as local effects. To quantitatively describe the effects, a model to determine near‐surface electric fields, incorporating space charge, and conductivity perturbations is developed. Statistical autonomous grouping of the mills using the spatial array demonstrates a greater than 50 V/m spatial variation from coastal to inland mills caused by wind‐advected space charge generated near the coast. A temporal analysis identified a strong, globally generated, diurnal signature, but only a weak annual signal is found. A realistic limit on conductivity reductions within clouds is estimated by analyzing overhead cloud cover in relation to near‐surface electric field strengths. The estimated in‐cloud conductivity reduction of approximately 1/3 is similar to observations but appreciably less than values estimated from microphysical cloud estimates. Finally, an enhancement in the electric field at sunrise is statistically well correlated with low wind speeds and high relative humidities. This paper provides a statistical description of local environmental effects on near‐surface electric fields by which to base future studies.
Real-time changes in rib cage expansion and use of abdominal mechanical stimulation in newborns: a quasi-experimental study

ABSTRACT Objective: To assess the rib cage expansion and respiratory rate in newborns using an abdominal stabilization band. Methods: The study included 32 newborns of both genders, with gestational age between 35 and 41 weeks. The abdominal stabilization band was used for 15 minutes between the xiphoid process and the anterosuperior iliac crest, with an abdominal contention 0.5cm smaller than the abdominal circumference. The rib cage expansion was evaluated by a breathing transducer (Pneumotrace II™) three minutes before using the band, during the use (15 minutes), and ten minutes after removing the band. The Shapiro-Wilk test verified data normality, and the Wilcoxon test compared the variables considering rib cage expansion and respiratory rate. Significance was set to p<0.05. Results: There was an increase in respiratory rate when comparing before and ten minutes after removing (p=0.008) the abdominal stabilization band, as well as when comparing during its use and ten minutes after its removal (p=0.001). There was also an increase in rib cage expansion when comparing before and during the use of the abdominal stabilization band (p=0.005). Conclusions: The use of the abdominal stabilization band promoted an increase in the rib cage expansion and respiratory rate in the assessed newborns and may be a viable option to improve the respiratory kinematics of this population.
Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome

Abstract Abundant ribonucleoside-triphosphate (rNTP) incorporation into DNA by DNA polymerases in the form of ribonucleoside monophosphates (rNMPs) is a widespread phenomenon in nature, resulting in DNA-structural change and genome instability. The rNMP distribution, characteristics, hotspots and association with DNA metabolic processes in human mitochondrial DNA (hmtDNA) remain mostly unknown. Here, we utilize the ribose-seq technique to capture embedded rNMPs in hmtDNA of six different cell types. In most cell types, the rNMPs are preferentially embedded on the light strand of hmtDNA with a strong bias towards rCMPs; while in the liver-tissue cells, the rNMPs are predominately found on the heavy strand. We uncover common rNMP hotspots and conserved rNMP-enriched zones across the entire hmtDNA, including in the control region, which links the rNMP presence to the frequent hmtDNA replication-failure events. We show a strong correlation between coding-sequence size and rNMP-embedment frequency per nucleotide on the non-template, light strand in all cell types, supporting the presence of transient RNA-DNA hybrids preceding light-strand replication. Moreover, we detect rNMP-embedment patterns that are only partly conserved across the different cell types and are distinct from those found in yeast mtDNA. The study opens new research directions to understand the biology of hmtDNA and genomic rNMPs.