Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Source Tracking Approach to Investigate Fecal Waste at the Strawberry Creek Watershed and Clam Beach, California, USA

Clam Beach is located in Northern California, USA, and is listed as an impaired waterway by the federal government. The scope of this study was to investigate this beach and surrounding watershed to determine, if possible, the source of the impairment by conducting an 11-h beach study and 8-week watershed study. We used traditional fecal indicator bacteria (FIB) and microbial source tracking (MST) methods to help identify source(s) of the FIB. Our study was focused on four possible contributors: human, ruminant, canine, and bird. A total of 169 samples were collected, analyzed, and compared to the California Department of Health single sample maximum (SSM) objective. In the beach study, 29 (44%) samples exceeded at least one SSM objective, which would have resulted in a resample per state regulations for recreational primary contact use. MST methods showed that the most abundant marker detected was bird, in 65% of the samples, but varied by sample location, which is likely due to a natural population of nearshore birds regularly observed along Clam Beach. The watershed study highlighted the potential influence from ruminants throughout the region, while humans did not appear to be a significant contributor. Health risk to humans appears to be low.
The Effect of Humic Mineral Substances from Oxyhumolite on the Coagulation Properties and Mineral Content of the Milk of Holstein-Friesian Cows

Simple Summary Global commodity milk production relies mainly on Holstein-Friesian cows. Intensive selection has made this breed highly productive, but deterioration of health, reduced longevity, and problems with milk quality have been observed. Much of the milk produced is used for cheese production, where its coagulation capacity is crucial. Dietary modifications are used to improve the health and milk quality of cows. Recent years have seen growing interest in humic substances in animal diets. Humic substances are natural organic substances formed in soil during humification of dead organic matter. Their main components are humic acids, fulvic acids and humins. Moreover, humic substances are a rich source of easily absorbed minerals. They are considered natural and safe feed additives with a number of positive effects, including improve of animal welfare and the quality of animal products. The literature lacks information on the results of the use of humic mineral substances in the diet of cows on the suitability of milk for cheese production. Therefore, the aim of the study was to assess the effect of the addition of humic mineral substances from oxyhumolite to the diet of high-producing cows on the chemical composition, mineral content and rennet clotting ability of milk. Abstract The study was conducted to determine the effect of humic mineral substances from oxyhumolite added to the diet of Holstein-Friesian cows on the coagulation properties, proximate chemical composition, and mineral profile of milk. The experiment was conducted on 64 cows divided into two groups of 32 each, control (CON) and experimental (H). The group H cows received the humic mineral substances as feed additive, containing 65% humic acids, for 60 days (100 g cow/day). Milk samples were collected twice, after 30 and 60 days. After 30 days no significant changes were observed in the chemical composition, somatic cell count (SCC), mineral content (except potassium), or curd texture parameters. However, the coagulation properties improved. The milk from group H after both 30 and 60 days coagulated significantly (15%) faster on average (p < 0.05), and the curd was about 36% and 28% firmer after 30 and 60 days, respectively (p < 0.05). After 60 days there was an increase in the content of fat (by 0.27 p.p.; p = 0.041), protein (by 0.14 p.p.; p = 0.012), and casein (by 0.12 p.p.; p = 0.029). SCC decreased by 20% (p = 0.023). The curds were significantly harder and less fracturable compared to the control. Calcium and iron content increased as well. The results indicate that humic mineral substances from oxyhumolite in the diet of cows can improve the suitability of milk for cheese production.
A Personalized Mass Spectrometry–Based Assay to Monitor M-Protein in Patients with Multiple Myeloma (EasyM)

Purpose: M-protein is a well-established biomarker used for multiple myeloma monitoring. Current improvements in multiple myeloma treatment created the need to monitor minimal residual disease (MRD) with high sensitivity. Measuring residual levels of M-protein in serum by MS was established as a sensitive assay for disease monitoring. In this study we evaluated the performance of EasyM—a noninvasive, sensitive, MS-based assay for M-protein monitoring. Experimental Design: Twenty-six patients enrolled in MCRN-001 clinical trial of two high-dose alkylating agents as conditioning followed by lenalidomide maintenance were selected for the study. All selected patients achieved complete responses (CR) during treatment, whereas five experienced progressive disease on study. The M-protein of each patient was first sequenced from the diagnostic serum using our de novo protein sequencing platform. The patient-specific M-protein peptides were then measured by targeted MS assay to monitor the response to treatment. Results: The M-protein doubling over 6 months measured by EasyM could predict the relapse in 4 of 5 relapsed patients 2 to 11 months earlier than conventional testing. In 21 disease-free patients, the M-protein was still detectable by EasyM despite normal FLC and MRD negativity. Importantly, of 72 MRD negative samples with CR status, 62 were positive by EasyM. The best sensitivity achieved by EasyM, detecting 0.58 mg/L of M-protein, was 1,000- and 200-fold higher compared with serum protein electrophoresis and immunofixation electrophoresis, respectively. Conclusions: EasyM was demonstrated to be a noninvasive, sensitive assay with superior performance compared with other assays, making it ideal for multiple myeloma monitoring and relapse prediction.
Effect of Heat Input on the Ballistic Performance of Armor Steel Weldments

The purpose of this study is to examine the projectile penetration resistance of the base metal and heat-affected zones of armor steel weldments. To ensure the proper quality of armor steel welded joints and associated ballistic protection, it is important to find the optimum heat input for armor steel welding. A total of two armor steel weldments made at heat inputs of 1.29 kJ/mm and 1.55 kJ/mm were tested for ballistic protection performance. The GMAW welding carried out employing a robot-controlled process. Owing to a higher ballistic limit, the heat-affected zone (HAZ) of the 1.29 kJ/mm weldment was found to be more resistant to projectile penetration than that of the 1.55 kJ/mm weldment. The ballistic performance of the weldments was determined by analyzing the microstructure of weldment heat-affected zones, the hardness gradients across the weldments and the thermal history of the welding heat inputs considered. The result showed that the ballistic resistance of heat affected zone exist as the heat input was decreased on 1.29 kJ/mm. It was found that 1.55 kJ/mm does not have ballistic resistance.
Impact of Endoscopic Ultrasound-Guided Tissue Acquisition on Decision-Making in Precision Medicine for Pancreatic Cancer: Beyond Diagnosis

Precision medicine in cancer treatment refers to targeted therapy based on the evaluation of biomarkers. Although precision medicine for pancreatic cancer (PC) remains challenging, novel biomarker-based therapies, such as pembrolizumab, olaparib, and entrectinib, have been emerging. Most commonly, endoscopic ultrasound-guided tissue acquisition (EUS-TA) had been used for the diagnosis of PC until now. However, advances in EUS-TA devices and biomarker testing, especially next-generation sequencing, have opened up the possibility of sequencing of various genes even in limited amounts of tissue samples obtained by EUS-TA, and identifying potential genetic alterations as therapeutic targets. Precision medicine benefits only a small population of patients with PC, but biomarker-based therapy has shown promising results in patients who once had no treatment options. Now, the role of EUS-TA has extended beyond diagnosis into decision-making regarding the treatment of PC. In this review, we mainly discuss tissue sampling by EUS-TA for biomarker testing and the current status of precision medicine for PC.
Modeling the Influence of Particulate Protein Size on Hydrolysis in Anaerobic Digestion

Batch experiments were performed to investigate the effect of particulate protein size on the hydrolysis of casein in anaerobic degradation. Whereas particle size did not affect the ultimate protein degradation efficiency, the hydrolysis rate coefficient increased from 0.034 to 0.298 day–1 with a change in specific surface area from 0.01 to 0.192 m2/g. The maximum rate of methane production increased from 6 to 14 mL of CH4 per gram of COD added per day with the same change in specific surface area, although the ultimate volume of methane produced was approximately the same despite the change in specific surface area. A mathematical relationship between the hydrolysis rate coefficient and the specific surface area was developed, and a new hydrolysis equation was proposed and verified.
Electrophysiological Evaluation of Pacific Oyster (Crassostrea gigas) Sensitivity to Saxitoxin and Tetrodotoxin

Pacific oysters (Crassostrea gigas) may bio-accumulate high levels of paralytic shellfish toxins (PST) during harmful algal blooms of the genus Alexandrium. These blooms regularly occur in coastal waters, affecting oyster health and marketability. The aim of our study was to analyse the PST-sensitivity of nerves of Pacific oysters in relation with toxin bio-accumulation. The results show that C. gigas nerves have micromolar range of saxitoxin (STX) sensitivity, thus providing intermediate STX sensitivity compared to other bivalve species. However, theses nerves were much less sensitive to tetrodotoxin. The STX-sensitivity of compound nerve action potential (CNAP) recorded from oysters experimentally fed with Alexandrium minutum (toxic-alga-exposed oysters), or Tisochrysis lutea, a non-toxic microalga (control oysters), revealed that oysters could be separated into STX-resistant and STX-sensitive categories, regardless of the diet. Moreover, the percentage of toxin-sensitive nerves was lower, and the STX concentration necessary to inhibit 50% of CNAP higher, in recently toxic-alga-exposed oysters than in control bivalves. However, no obvious correlation was observed between nerve sensitivity to STX and the STX content in oyster digestive glands. None of the nerves isolated from wild and farmed oysters was detected to be sensitive to tetrodotoxin. In conclusion, this study highlights the good potential of cerebrovisceral nerves of Pacific oysters for electrophysiological and pharmacological studies. In addition, this study shows, for the first time, that C. gigas nerves have micromolar range of STX sensitivity. The STX sensitivity decreases, at least temporary, upon recent oyster exposure to dinoflagellates producing PST under natural, but not experimental environment.
Influence of Deposition Method on the Structural and Optical Properties of Ge2Sb2Te5

Ge2Sb2Te5 (GST-225) is a chalcogenide material with applications in nonvolatile memories. However, chalcogenide material properties are dependent on the deposition technique. GST-225 thin films were prepared using three deposition methods: magnetron sputtering (MS), pulsed laser deposition (PLD) and a deposition technique that combines MS and PLD, namely MSPLD. In the MSPLD technique, the same bulk target is used for sputtering but also for PLD at the same time. The structural and optical properties of the as-deposited and annealed thin films were characterized by Rutherford backscattering spectrometry, X-ray reflectometry, X-ray diffraction, Raman spectroscopy and spectroscopic ellipsometry. MS has the advantage of easily leading to fully amorphous films and to a single crystalline phase after annealing. MS also produces the highest optical contrast between the as-deposited and annealed films. PLD leads to the best stoichiometric transfer, whereas the annealed MSPLD films have the highest mass density. All the as-deposited films obtained with the three methods have a similar optical bandgap of approximately 0.7 eV, which decreases after annealing, mostly in the case of the MS sample. This study reveals that the properties of GST-225 are significantly influenced by the deposition technique, and the proper method should be selected when targeting a specific application. In particular, for electrical and optical phase change memories, MS is the best suited deposition method.
Nitric Oxide Interaction with the Eye

Nitric oxide (NO) is acknowledged as a vital intercellular messenger in multiple systems in the body. Medicine has focused on its functions and therapeutic applications for decades, especially in cardiovascular and nervous systems, and its role in immunological responses. This review was composed to demonstrate the prevalence of NO in components of the ocular system, including corneal cells and multiple cells in the retina. It discussed NO’s assistance during the immune, inflammation and wound-healing processes. NO is identified as a vascular endothelial relaxant that can alter the choroidal blood flow and prompt or suppress vascular changes in age-related macular degeneration and diabetes, as well as the blood supply to the optic nerve, possibly influencing the progression of glaucoma. It will provide a deeper understanding of the role of NO in ocular homeostasis, the delicate balance between overproduction or underproduction and the effect on the processes from aqueous outflow and subsequent intraocular pressure to axial elongation and the development of myopia. This review also recognized the research and investigation of therapies being developed to target the NO complex and treat various ocular diseases.
Anticancer Potential of Temozolomide-Loaded Eudragit-Chitosan Coated Selenium Nanoparticles: In Vitro Evaluation of Cytotoxicity, Apoptosis and Gene Regulation

Resistance to temozolomide (TMZ) is the main cause of death in glioblastoma multiforme (GBM). The use of nanocarriers for drug delivery applications is one of the known approaches to overcome drug resistance. This study aimed to investigate the possible effect of selenium–chitosan nanoparticles loaded with TMZ on the efficacy of TMZ on the expression of MGMT, E2F6, and RELA genes and the rate of apoptosis in the C6 cell line. Selenium nanoparticles (SNPs) were loaded with TMZ and then they were coated by Eudragit® RS100 (Eud) and chitosan (CS) to prepare Se@TMZ/Eud-Cs. Physicochemical properties were determined by scanning electron microscope (SEM), energy-dispersive X-ray spectroscopy (EDAX), thermal gravimetric analysis (TGA), Fourier-transform infrared spectroscopy (FTIR), and dynamic light scattering (DLS) methods. Se@TMZ/Eud-Cs was evaluated for loading and release of TMZ by spectrophotometric method. Subsequently, SNPs loaded with curcumin (as a fluorophore) were analyzed for in vitro uptake by C6 cells. Cytotoxicity and apoptosis assay were measured by MTT assay and Annexin-PI methods. Finally, real-time PCR was utilized to determine the expression of MGMT, E2F6, and RELA genes. Se@TMZ/Eud-Cs was prepared with an average size of 200 nm as confirmed by the DLS and microscopical methods. Se@TMZ/Eud-Cs presented 82.77 ± 5.30 loading efficiency with slow and pH-sensitive release kinetics. SNPs loaded with curcumin showed a better uptake performance by C6 cells compared with free curcumin (p-value < 0.01). Coated nanoparticles loaded with TMZ showed higher cytotoxicity, apoptosis (p-value < 0.0001), and down-regulation of MGMT, E2F6, and RELA and lower IC50 value (p-value < 0.0001) than free TMZ and control (p-value < 0.0001) groups. Using Cs as a targeting agent in Se@TMZ/Eud-Cs system improved the possibility for targeted drug delivery to C6 cells. This drug delivery system enhanced the apoptosis rate and decreased the expression of genes related to TMZ resistance. In conclusion, Se@TMZ/Eud-Cs may be an option for the enhancement of TMZ efficiency in GBM treatment.
Effects of nintedanib by inclusion criteria for progression of interstitial lung disease

Background The INBUILD trial investigated nintedanib versus placebo in patients with progressive fibrosing interstitial lung diseases (ILDs). We investigated the decline in forced vital capacity (FVC) in subgroups based on the inclusion criteria for ILD progression. Methods Subjects had a fibrosing ILD other than idiopathic pulmonary fibrosis and met the following criteria for ILD progression within the 24 months before screening despite management deemed appropriate in clinical practice: Group A, relative decline in FVC ≥10% predicted; Group B, relative decline in FVC ≥5–<10% predicted with worsened respiratory symptoms and/or increased extent of fibrosis on high-resolution computed tomography (HRCT); Group C, worsened respiratory symptoms and increased extent of fibrosis on HRCT only. Results In the placebo group, the rates of FVC decline over 52 weeks in Groups A, B and C, respectively, were −241.9, −133.1 and −115.3 mL per year in the overall population (p=0.0002 for subgroup-by-time interaction) and −288.9, −156.2 and −100.1 mL per year among subjects with a usual interstitial pneumonia (UIP)-like fibrotic pattern on HRCT (p=0.0005 for subgroup-by-time interaction). Nintedanib had a greater absolute effect on reducing the rate of FVC decline in Group A than in Group B or C. However, the relative effect of nintedanib versus placebo was consistent across the subgroups (p>0.05 for heterogeneity). Conclusions The inclusion criteria used in the INBUILD trial, based on FVC decline or worsening of symptoms and extent of fibrosis on HRCT, were effective at identifying patients with progressive fibrosing ILDs. Nintedanib reduced the rate of decline in FVC across the subgroups based on the inclusion criteria related to ILD progression. In the INBUILD trial in patients with fibrosing ILDs, the relative effect of nintedanib versus placebo on reducing the rate of FVC decline was consistent across subgroups based on the criteria regarding ILD progression that patients fulfilled on trial entry https://bit.ly/35jpOiE
Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites

Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, Halobacterium salinarum NRC-1 and Haloferax volcanii DS2. TPS were established by reanalysis of publicly available differential RNA-seq (dRNA-seq) data, searching for non-primary (monophosphorylated RNAs) enrichment. We found 2093 TPS in 43% of H. salinarum genes and 3515 TPS in 49% of H. volcanii chromosomal genes. Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. Examples include the cell division gene ftsZ2, whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS200/IS605. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface.
Investigation of the Effects of Electrode Geometry on the Performance of C4D Sensor with Radial Configuration

Electrodes are basic components of C4D (capacitively coupled contactless conductivity detection) sensors, and different electrode structures (the configuration pattern or the electrode geometry) can lead to different measurement results. In this work, the effects of electrode geometry of radial configuration on the measurement performance of C4D sensors are investigated. Two geometrical parameters, the electrode length and the electrode angle, are considered. A FEM (finite element method) model based on the C4D method is developed. With the FEM model, corresponding simulation results of conductivity measurement with different electrode geometry are obtained. Meanwhile, practical experiments of conductivity measurement are also conducted. According to the simulation results and experimental results, the optimal electrode geometry of the C4D sensor with radial configuration is discussed and proposed. The recommended electrode length is 5–10 times of the pipe inner diameter and the recommended electrode angle is 120–160°.
Conspecific and congeneric interactions shape increasing rates of breeding dispersal of northern spotted owls

Abstract Breeding dispersal, the movement from one breeding territory to another, is rare for philopatric species that evolved within relatively stable environments, such as the old‐growth coniferous forests of the Pacific Northwest. Although dispersal is not inherently maladaptive, the consequences of increased dispersal on population dynamics in populations whose historical dispersal rates are low could be significant, particularly for a declining species. We examined rates and possible causes of breeding dispersal based on a sample of 4,118 northern spotted owls (Strix occidentalis caurina) monitored in seven study areas over 28 yr, 1990–2017, in Oregon and Washington, USA. Using a multistate mark–resight analysis, we investigated the potential impacts of an emergent congeneric competitor (barred owl Strix varia) and forest alteration (extrinsic factors), and social and individual conditions (intrinsic factors) on 408 successive and 1,372 nonsuccessive dispersal events between years. The annual probability of breeding dispersal increased for individual owls that had also dispersed in the previous year and decreased for owls on territories with historically high levels of reproduction. Intrinsic factors including pair status, prior reproductive success, and experience at a site, were also associated with breeding dispersal movements. The percent of monitored owls dispersing each year increased from ˜7% early in the study to ˜25% at the end of the study, which coincided with a rapid increase in numbers of invasive and competitively dominant barred owls. We suggest that the results presented here can inform spotted owl conservation efforts as we identify factors contributing to changing rates of demographic parameters including site fidelity and breeding dispersal. Our study further shows that increasing rates of breeding dispersal associated with population declines contribute to population instability and vulnerability of northern spotted owls to extinction, and the prognosis is unlikely to change unless active management interventions are undertaken.