Miracle-dz/UniFAR-FTUs huggingface dataset:
Microfluidic sorting of protein nanocrystals by size for X-ray free-electron laser diffraction

The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10–100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also permit an analysis of the dependence of crystal quality on crystal size.
Genotoksični učinak anestetika sevoflurana i ionizirajućeg zračenja u miševa soja Swiss albino

Despite of many advantages of various medical aplications (i.e. radiotherapy), radiation can be harmful and it's well known as carcinogen for living organisms. The main biomolecule of interest is DNA. Sevoflurane is nonflammable, inhalation anesthetic which provides fast and efficient hypnosis with low accumulation in tissue and minimal irritation of respiratory tract. However, metabolism of sevoflurane may have an important influence for its toxicity. This research studied individual and combined effect of ionizing radiation (2 Gy) and sevoflurane (2,4 %) on DNA damage in peripheral blood leukocytes as well as in liver, kidney and brain cells of Swiss albino mice. Effect has been observed by alkaline comet assay immediately after, and 2, 6 and 24 hours after exposure to radiation and anesthesia. Results have shown that the most significant genotoxic effect in peripheral blood leukocytes and kidney cells was 2 hours after treatment, whilst in liver and brain cells the cytotoxicity was at the highest level 24 hours after exposure to these agents. Cell repair indeks, used to assess the difference in the amount of DNA repair among various cell types, shown that the least sensitive to treatment with genotoxic agents were peripheral blood leukocytes, and the most sensitive were liver cells.
Elimination of exogenously injected sodium‐hyaluronate from rabbit flexor tendon sheaths

To obtain information about the elimination of Na hyaluronate (NaHe) deposited in flexor tendon sheaths in rabbits, two flexor tendon sheaths from each hind limb were operatively exposed in 15 animals and each filled with one of four different NaHe preparations, namely: 10 mg/ml, MW 2.6 × 106; 10 mg/ml, MW 6.3 × 106; 19 mg/ml, MW 3.0 × 106; and 19 mg/ml, MW 6.5 × 106. One, 3, and 7 days after surgery, the NaHe concentration was measured in frozen specimens from the tendon sheaths. One day after surgery, NaHe concentration in the tendon sheath fluid was close to 10 mg/ml in all groups. Three and 7 days after surgery it was higher in tendon sheaths in which NaHe preparations with a high (19 mg/ml) rather than with a low concentration (10 mg/ml) had been deposited. At 3 days, NaHe concentration was also higher in sheaths that had received a preparation with a high MW (6.5 × 106) than those with a lower MW (2.6 or 3.0 × 106). The findings suggest that within the first 24 h, a dilution of concentrated NaHe preparations takes place, probably as a result of their hyperoncotic properties. After 24 h, there was a slower decline in NaHe concentration when more concentrated solutions (19 mg/ml) and solutions with high MWs (6.5 × 106) were administered. Development of pharmaceutical NaHe preparations with slow elimination from tendon sheaths should reasonably be focused on a solution with a high MW and high concentration.
The Role of Neutral Sphingomyelinase-2 (NSM2) in the Control of Neutral Lipid Storage in T Cells

The accumulation of lipid droplets (LDs) and ceramides (Cer) is linked to non-alcoholic fatty liver disease (NAFLD), regularly co-existing with type 2 diabetes and decreased immune function. Chronic inflammation and increased disease severity in viral infections are the hallmarks of the obesity-related immunopathology. The upregulation of neutral sphingomyelinase-2 (NSM2) has shown to be associated with the pathology of obesity in tissues. Nevertheless, the role of sphingolipids and specifically of NSM2 in the regulation of immune cell response to a fatty acid (FA) rich environment is poorly studied. Here, we identified the presence of the LD marker protein perilipin 3 (PLIN3) in the intracellular nano-environment of NSM2 using the ascorbate peroxidase APEX2-catalyzed proximity-dependent biotin labeling method. In line with this, super-resolution structured illumination microscopy (SIM) shows NSM2 and PLIN3 co-localization in LD organelles in the presence of increased extracellular concentrations of oleic acid (OA). Furthermore, the association of enzymatically active NSM2 with isolated LDs correlates with increased Cer levels in these lipid storage organelles. NSM2 enzymatic activity is not required for NSM2 association with LDs, but negatively affects the LD numbers and cellular accumulation of long-chain unsaturated triacylglycerol (TAG) species. Concurrently, NSM2 expression promotes mitochondrial respiration and fatty acid oxidation (FAO) in response to increased OA levels, thereby shifting cells to a high energetic state. Importantly, endogenous NSM2 activity is crucial for primary human CD4+ T cell survival and proliferation in a FA rich environment. To conclude, our study shows a novel NSM2 intracellular localization to LDs and the role of enzymatically active NSM2 in metabolic response to enhanced FA concentrations in T cells.
An intrinsically disordered C terminus allows the La protein to assist the biogenesis of diverse noncoding RNA precursors

The La protein binds the 3′ ends of many newly synthesized noncoding RNAs, protecting these RNAs from nucleases and influencing folding, maturation, and ribonucleoprotein assembly. Although 3′ end binding by La involves the N-terminal La domain and adjacent RNA recognition motif (RRM), the mechanisms by which La stabilizes diverse RNAs from nucleases and assists subsequent events in their biogenesis are unknown. Here we report that a conserved feature of La proteins, an intrinsically disordered C terminus, is required for the accumulation of certain noncoding RNA precursors and for the role of the Saccharomyces cerevisiae La protein Lhp1p in assisting formation of correctly folded pre-tRNA anticodon stems in vivo. Footprinting experiments using purified Lhp1p reveal that the C terminus is required to protect a pre-tRNA anticodon stem from chemical modification. Although the C terminus of Lhp1p is hypersensitive to proteases in vitro, it becomes protease-resistant upon binding pre-tRNAs, U6 RNA, or pre-5S rRNA. Thus, while high affinity binding to 3′ ends requires the La domain and RRM, a conformationally flexible C terminus allows La to interact productively with a diversity of noncoding RNA precursors. We propose that intrinsically disordered domains adjacent to well characterized RNA-binding motifs in other promiscuous RNA-binding proteins may similarly contribute to the ability of these proteins to influence the cellular fates of multiple distinct RNA targets.
Effects of routing computations in content-based routing networks with mobile data sources

This paper presents the first quantitative evaluation of the role of routing computations on performance when mobility is introduced to a content-based routing network. Additionally, the paper identifies the factors that affect the performance of a distributed publish/subscribe architecture supporting mobile publishers, formalizes publisher mobility protocols for distributed publish/subscribe systems, and develops and evaluates protocols that reduce the costs associated with supporting mobile publishers in publish/subscribe systems. Our results show that ignoring route computation time paints a false picture of the scalability of content-based routing networks, but that with appropriate protocols the adverse effects can be mitigated.
Design of Simulink Model For OSTBC And Performance Evaluation of Ieee 802.16 OFDM Phy Link With And Without Space-Time Block Coding For Wireless Communication

Because of the rapid growth of Digital Communication in recent years, the need for high speed data transmission is increased. Orthogonal frequency division multiplexing (OFDM) technique is suitable for high speed communication because of its resistance to ISI (inter symbol interference) and it utilizes the bandwidth efficiently. OSTBCs are an attractive technique for MIMO wireless communications. They exploit full spatial diversity order and enjoy symbol-wise maximum likelihood (ML) decoding. However, they offer no coding gain. The combiner for OSTBC at the receiver side provides soft information of the transmitted symbols, which can be utilized for decoding or demodulation of an outer code.TCM is a bandwidth efficient scheme that integrates coding and modulation to provide a large coding gain. Concatenating TCM with an inner code will usually offer an improved performance. This illustrates the advantages of an OSTBC and TCM concatenation scheme: the spatial diversity gain offered by OSTBC and the coding gain offered by TCM. For comparison, two reference models containing only TCM or OSTBC are also provided. The diversity and coding gains of the concatenation scheme over the reference models can be clearly observed from the simulation results. Also this includes an endto-end baseband model of the physical layer of a wireless metropolitan area network (WMAN), according to the IEEE® 802.16-2004 standard . More specifically, it models the OFDM-based physical layer, called Wireless MAN-OFDM, supporting all of the mandatory coding and modulation options.
Physiological pathway of differentiation of hematopoietic stem cell population into mural cells

Endothelial cells (ECs), which are a major component of blood vessels, have been reported to develop in adulthood from hematopoietic cell populations, especially those of the monocyte lineage. Here we show that mural cells (MCs), another component of blood vessels, develop physiologically during embryogenesis from a hematopoietic stem cell (HSC) population, based on the in vitro culture of HSCs and histological examination of acute myeloid leukemia 1 mutant embryos, which lack HSCs. As in the embryo, HSCs in adult bone marrow differentiate into CD45+CD11b+ cells before differentiating into MCs. Moreover, CD45+CD11b+ cells are composed of two populations, CD11bhigh and CD11blow cells, both of which can differentiate into MCs as well as ECs. Interestingly, in a murine ischemia model, MCs and ECs derived from the CD11blow population had a long-term potential to contribute to the formation of newly developed blood vessels in vivo compared with the CD11high population, which could not. Moreover, injection of the CD11bhigh population induced leaky blood vessels, but the CD11blow population did not. With respect to the permeability of vessels, we found that angiopoietin 1, which is a ligand for Tie2 receptor tyrosine kinase expressed on ECs and is suggested to induce cell adhesion between ECs and MCs, is produced by the CD11blow population and plays a critical role in the formation of nonleaky vessels. These observations suggested that the CD11low cell population serves as a good source of cells for in vivo blood vessel regeneration.
Visual‐interactive Exploration of Interesting Multivariate Relations in Mixed Research Data Sets

The analysis of research data plays a key role in data‐driven areas of science. Varieties of mixed research data sets exist and scientists aim to derive or validate hypotheses to find undiscovered knowledge. Many analysis techniques identify relations of an entire dataset only. This may level the characteristic behavior of different subgroups in the data. Like automatic subspace clustering, we aim at identifying interesting subgroups and attribute sets. We present a visual‐interactive system that supports scientists to explore interesting relations between aggregated bins of multivariate attributes in mixed data sets. The abstraction of data to bins enables the application of statistical dependency tests as the measure of interestingness. An overview matrix view shows all attributes, ranked with respect to the interestingness of bins. Complementary, a node‐link view reveals multivariate bin relations by positioning dependent bins close to each other. The system supports information drill‐down based on both expert knowledge and algorithmic support. Finally, visual‐interactive subset clustering assigns multivariate bin relations to groups. A list‐based cluster result representation enables the scientist to communicate multivariate findings at a glance. We demonstrate the applicability of the system with two case studies from the earth observation domain and the prostate cancer research domain. In both cases, the system enabled us to identify the most interesting multivariate bin relations, to validate already published results, and, moreover, to discover unexpected relations.
Human‐induced seismicity and large‐scale hydrocarbon production in the USA and Canada

We compare current and historic seismicity rates in six States in the USA and three Provinces in Canada to past and present hydrocarbon production. All States/Provinces are major hydrocarbon producers. Our analyses span three to five decades depending on data availability. Total hydrocarbon production has significantly increased in the past few years in these regions. Increased production in most areas is due to large‐scale hydraulic fracturing and thus underground fluid injection. Furthermore, increased hydrocarbon production generally leads to increased water production, which must be treated, recycled, or disposed of underground. Increased fluid injection enhances the likelihood of fault reactivation, which may affect current seismicity rates. We find that increased seismicity in Oklahoma, likely due to salt‐water disposal, has an 85% correlation with oil production. Yet, the other areas do not display State/Province‐wide correlations between increased seismicity and production, despite 8–16‐fold increases in production in some States. However, in various cases, seismicity has locally increased. Multiple factors play an important role in determining the likelihood of anthropogenic activities influencing earthquake rates, including (i) the near‐surface tectonic background rate, (ii) the existence of critically stressed and favorably oriented faults, which must be hydraulically connected to injection wells, (iii) the orientation and magnitudes of the in situ stress field, combined with (iv) the injection volumes and implemented depletion strategies. A comparison with the seismic hazard maps for the USA and Canada shows that induced seismicity is less likely in areas with a lower hazard. The opposite, however, is not necessarily true.
Regulators of G-Protein Signaling 10 and Heart Failure: The Importance of Negative Regulators of Heart Disease.

See related article, pp 86–98 Heart failure involves changes in cardiac structure, myocardial composition, myocyte deformation, and multiple biochemical and molecular alterations that impact heart function, collectively referred to as adverse cardiac remodeling.1,2 Left ventricular remodeling is a complex process involving cardiac myocyte growth and death, vascular rarefaction, cardiac fibrosis, inflammation, alterations in cardiac energetics, and electrophysiological remodeling. Recently, several endogenous negative regulators of cardiac hypertrophy have been discovered, which are basally inactive and becomes activated in response to a pathological stimulus. Understanding the mechanisms of activation of these endogenous negative regulators and their target positive regulators will allow the development of novel therapeutic strategies.3 Regulators of G protein signaling (RGS) family proteins are such negative regulators which primarily fine-tune G protein–coupled receptor (GPCR)–induced signaling by regulating its magnitude and duration through direct interaction with the alpha subunits of heterotrimeric G proteins. Miao et al studied the novel role of RGS10 in heart failure by using 2 mutant murine models, RGS10 overexpression and knockout (KO), and showed RGS10-mediated regulation of Gαq/11 plays a crucial role in the maintenance of heart function.4 Signal transduction through the activation of GPCRs is a dominant mechanism for the regulation of cardiovascular physiology, including the regulation of heart rate, myocardial hypertrophy, and contractility, and vascular tone. The success of pharmaceuticals that inhibit β-adrenergic receptors and AT1 receptors, which represent stereotypical GPCRs, also demonstrate the importance of these signaling pathways in disease pathogenesis. Ligand-induced activation of GPCR results into the exchange of guanosine diphosphate and guanosine triphosphate on the alpha subunit, which then dissociates from the βγ-subunit and, in turn, activates the respective downstream targets, leading to cellular responses. The activity of the GPCR is terminated when alpha subunit’s intrinsic guanosine triphosphatase activity hydrolyses the guanosine triphosphate to guanosine diphosphate, and …
The Anticancer, Antioxidant and Antimicrobial Properties of the Sesquiterpene β-Caryophyllene from the Essential Oil of Aquilaria crassna

The present study reports a bioassay-guided isolation of β-caryophyllene from the essential oil of Aquilaria crassna. The structure of β-caryophyllene was confirmed using FT-IR, NMR and MS. The antimicrobial effect of β-caryophyllene was examined using human pathogenic bacterial and fungal strains. Its anti-oxidant properties were evaluated by DPPH and FRAP scavenging assays. The cytotoxicity of β-caryophyllene was tested against seven human cancer cell lines. The corresponding selectivity index was determined by testing its cytotoxicity on normal cells. The effects of β-caryophyllene were studied on a series of in vitro antitumor-promoting assays using colon cancer cells. Results showed that β-caryophyllene demonstrated selective antibacterial activity against S. aureus (MIC 3 ± 1.0 µM) and more pronounced anti-fungal activity than kanamycin. β-Caryophyllene also displayed strong antioxidant effects. Additionally, β-caryophyllene exhibited selective anti-proliferative effects against colorectal cancer cells (IC50 19 µM). The results also showed that β-caryophyllene induces apoptosis via nuclear condensation and fragmentation pathways including disruption of mitochondrial membrane potential. Further, β-caryophyllene demonstrated potent inhibition against clonogenicity, migration, invasion and spheroid formation in colon cancer cells. These results prompt us to state that β-caryophyllene is the active principle responsible for the selective anticancer and antimicrobial activities of A. crassnia. β-Caryophyllene has great potential to be further developed as a promising chemotherapeutic agent against colorectal malignancies.
318 Lumbar Disc Surgery: Clinical Outcome of 85 Patients With a Mean Follow-up of 32 Years.

INTRODUCTION Surgery of lumbar disc herniation is one of the most common neurosurgical procedures. Since the introduction of the microscope, the so-called microscopic discectomy (MD) has represented the "gold standard" technique until today. Here, the authors present clinical outcome of patients treated for of lumbar disc herniation with a mean follow-up of more than 30 years. METHODS A retrospective outcome study enrolled 85 patients who underwent a 1- to 2-level MD or standard open discectomy (SOD) 27 to 40 years ago. The pre- and postoperative clinical status and the surgical record were analyzed for all patients. A standardized questionnaire which included the current neurological status, EQ-5D, PSI, Odom criteria, Oswestry Disability Index (ODI), and limitations in quality of life because of the operation was answered by each patient. RESULTS The mean follow-up was 32.1 years, 50 patients were operated on via MD, and 35 via SOD. Preoperatively, the mean pain intensity for leg pain was 9 on the Numeric Pain Rating Scale (NPRS), and 1 at follow-up. Median EQ-5D was 6, according to PSI 93% of the patients were satisfied, according to Odom criteria 91% of the patients reported good-to-excellent functional recovery. The mean ODI was 15% (range 0-60%). Eight patients had a second surgery because of recurrent disc herniation, 13 patients had a second surgery because of a new disc herniation at the adjacent level. Two patients underwent a third procedure. The recurrent herniation rate was 8% in the MD group and 12% in SOD group. CONCLUSION The long-term follow-up data of this study reveals excellent clinical results even after more than 30 years. Overall rate for second surgery was 25%. About 15% of all patients needed a second surgery because of a disc herniation at the adjacent segment. No difference in long-term clinical outcome could be demonstrated for microdiscectomy and open discectomy.