gebhart/patrepeval huggingface dataset:
The cohesin module is a major determinant of cellulosome mechanical stability (2018)

Cellulosomes are bacterial protein complexes that bind and efficiently degrade lignocellulosic substrates. These are formed by multimodular scaffolding proteins known as scaffoldins, which comprise cohesin modules capable of binding dockerin-bearing enzymes and usually a carbohydrate-binding module that anchors the system to a substrate. It has been suggested that cellulosomes bound to the bacterial cell surface might be exposed to significant mechanical forces. Accordingly, the mechanical properties of these anchored cellulosomes may be important to understand and improve cellulosome function. Here we used single-molecule force spectroscopy to study the mechanical properties of selected cohesin modules from scaffoldins of different cellulosomes. We found that cohesins located in the region connecting the cell and the substrate are more robust than those located outside these two anchoring points. This observation applies to cohesins from primary scaffoldins (<i>i.e.</i> those that directly bind dockerin-bearing enzymes) from different cellulosomes despite their sequence differences. Furthermore, we also found that cohesin nanomechanics (specifically, mechanostability and the position of the mechanical clamp of cohesin) are not significantly affected by other cellulosomal components, including linkers between cohesins, multiple cohesin repeats, and dockerin binding. Finally, we also found that cohesins (from both the connecting and external regions) have poor refolding efficiency but similar refolding rates, suggesting that the high mechanostability of connecting cohesins may be an evolutionarily conserved trait selected to minimize the occurrence of cohesin unfolding, which could irreversibly damage the cellulosome. We conclude that cohesin mechanostability is a major determinant of the overall mechanical stability of the cellulosome.
Threshold catalytic onset of carbon formation on CeO 2 during CO 2 electrolysis: mechanism and inhibition (2019)

Carbon deposition from CO and other carbon-containing fuels is a major cause of the performance degradation of catalysts and electrocatalysts in many energy conversion devices, including low-temperature solid oxide cells (LT-SOCs). In this work, we present direct observation of carbon deposition on thin-film CeO2 electrodes at LT-SOC operating temperatures (450 °C) in a CO/CO2 atmosphere by in operando X-ray photoelectron spectroscopy. In contrast to the general view that CeO2 is a carbon tolerant material, significant carbon formation was observed on CeO2 during CO2 electrolysis, with no other catalyst present. Moreover, carbon deposition on CeO2 demonstrated an intriguing threshold onset formation against surface Ce3+ concentration. With the aid of Monte Carlo simulations, we propose the neighboring Ce3+-Ce3+ pairs to be a critical catalytic structure that facilitates carbon deposition from CO. Finally, we propose mitigation of carbon deposition on CeO2 by doping CeO2 with non-redox-active cations, and proved this concept using 50% Gd- and 50% Zr-doped CeO2 as an example system. These findings provide an in-depth understanding of the mechanism of carbon deposition on CeO2 during electrochemical reactions and can guide the design of carbon-resistant CeO2-based electrocatalysts.
Candidate proteomic biomarkers for three genogroups of the swine pathogen Streptococcus suis serotype 2 (2015)

SELDI analysis of 45 strains of S. suis allowed to identify nine statistically significant proteins that can be specifically correlated with either ST1, ST25 or ST28. The possible involvement of the overexpressed proteins in the pathology of S. suis infections will require further investigation.
Increased Biobutanol Production by Mediator‐Less Electro‐Fermentation (2018)

A future bio-economy should not only be based on renewable raw materials but also in the raise of carbon yields of existing production routes. Microbial electrochemical technologies are gaining increased attention for this purpose. In this study, the electro-fermentative production of biobutanol with C. acetobutylicum without the use of exogenous mediators is investigated regarding the medium composition and the reactor design. It is shown that the use of an optimized synthetic culture medium allows higher product concentrations, increased biofilm formation, and higher conductivities compared to a synthetic medium supplemented with yeast extract. Moreover, the optimization of the reactor system results in a doubling of the maximum product concentrations for fermentation products. When a working electrode is polarized at -600 mV vs. Ag/AgCl, a shift from butyrate to acetone and butanol production is induced. This leads to an increased final solvent yield of Y<sub>ABE</sub> = 0.202 g g<sup>-1</sup> (control 0.103 g g<sup>-1</sup> ), which is also reflected in a higher carbon efficiency of 37.6% compared to 23.3% (control) as well as a fourfold decrease in simplified E-factor to 0.43. The results are promising for further development of biobutanol production in bioelectrochemical systems in order to fulfil the principles of Green Chemistry.
Abstract 1574: Circadian clock gene expression and lethal prostate cancer outcomes (2019)

Abstract Background: Converging evidence points to a potential role of disruption of the circadian rhythm in prostate cancer progression. There is limited human data in prostate tissue examining the biological consequences of alterations in genes involved in circadian rhythm on outcomes among prostate cancer patients. Methods: To test the hypothesis that tissue expression of circadian-related genes was associated with prostate cancer outcomes, we leveraged data from the Physicians' Health Study (PHS) and the Health Professionals Follow-Up Study (HPFS) prostate tumor cohorts. Whole transcriptome expression profiling was performed on 404 prostate cancer cases, including 113 lethal cases (metastatic disease or prostate cancer death) and 291 indolent cases (&amp;gt;8 years from diagnosis without evidence of metastasis). Using logistic regression models, we assessed whether mRNA expression levels in tumor (N=404) or paired normal prostate tissue (N=202) of eleven circadian-related genes (AANAT, CLOCK, CRY1, CRY2, CSNK1E, MTNR1B, NPAS2, OPN4, PER1, PER2, PER3) were associated with lethal prostate cancer, stage (T2 vs. T3+), Gleason grade at diagnosis (&amp;lt;8 vs. ≥8), and biomarkers of angiogenesis and apoptosis. We calculated odds ratios and 95% confidence intervals (95% CIs) per standard deviation increase in gene expression. Results: Pathway analyses showed a statistically significant association between the eleven circadian genes and lethal disease (global test p-value = 5.1e-05). On an individual gene level, men with higher tumor expression of Period Circadian Regulator 1 (PER1) gene had a reduced risk of lethal disease, independent of grade and stage (OR: 0.75, 95% CI: 0.59-0.97). High tumor expression of PER1 (OR: 0.72, 95% CI: 0.57-0.91) and Cryptochrome Circadian Regulator 2 (CRY2) (OR: 0.79, 95% CI: 0.63-1.00) were associated with lower Gleason grade tumors. High tumor expression of PER1 was associated with lower levels of cell proliferation and lower levels of angiogenesis markers; Neuronal PAS Domain Protein 2 (NPAS2) was associated with markers of apoptosis. For none of the genes was expression in normal prostate tissue associated with lethal prostate cancer (global test p-value = 0.06). Discussion: We found higher expression of several of the circadian related genes were associated with less aggressive prostate cancer features. In line with these findings, PER1 has been suggested to be a tumor suppressor in previous studies. This supports the idea that maintenance of circadian clock function may protect tumor progression. Citation Format: Sarah C. Markt, Ericka Ebot, Iona Cheng, Lynne Wilkens, Ayesha Shafi, Karen Knudsen, Kathryn Penney, Lorelei Mucci, Travis Gerke. Circadian clock gene expression and lethal prostate cancer outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1574.
The Declining Use of Wrist-Spanning External Fixators (2018)

<b>Background:</b> External fixation has been traditionally used to treat comminuted or open distal radius fractures that are not amenable to open reduction internal fixation. This procedure is associated with a relatively high complication rate and has been used with decreasing frequency in recent years. However, trends in external fixation utilization for the treatment of distal radius fractures have not been described. <b>Methods:</b> Using the Nationwide Inpatient Sample, patients with a distal radius fracture treated with external fixation from 2003 to 2014 were identified. The annual incidence was reported, and hospital and demographic variables associated with external fixation use were determined. <b>Results:</b> During the study period, 593 929 patients with a distal radius fracture were identified, of which 51 766 (8.7%) were treated with a wrist-spanning external fixator. Wrist external fixation for the treatment of distal radius fractures declined steadily from 2003 to 2014. In 2003, external fixation use was highest, accounting for 17.4% of distal radius fractures. By 2014, only 4.9% of distal radius fracture were treated with external fixation. During this period, the incidence of distal radius fractures declined by 6.9% while external fixator utilization decreased by 73.7%. Patients receiving an external fixator were more likely to be male, low-income, and treated in a rural, nonteaching, privately owned hospital. <b>Conclusions:</b> External fixator use for the treatment of distal radius fractures steadily declined during the study period. Males and those with lower incomes treated in rural, nonteaching, and privately owned hospitals are more likely to receive external fixation.
Performance Assessment and Feasibility Analysis of IEEE 802.15.4m Wireless Sensor Networks in TV Grayspaces (2017)

In this article, we assess the viability of underlay sensor networks in frequencies used by an incumbent digital TV broadcasting system, that is, in the so-called TV grayspaces (TVGS). Grayspace operations are particularly interesting when other unlicensed bands are overcrowded, for example, due to high-volume WiFi operations. We simulate the operational characteristics of the recent IEEE 802.15.4m standard for low-rate wireless personal area networks to evaluate the performance degradation of an incumbent Digital Video Broadcasting - Terrestrial (DVB-T) system if a secondary network of low-power low-rate devices are co-deployed in the same frequency bands. Our results show that short sensor messages will not disrupt the DVB-T service due to the existing error-correction capabilities. Furthermore, if sufficient separation distances to primary transmitters are maintained, transmit powers are sufficient to achieve reasonable connectivity levels of the secondary network. In order to obtain realistic figures on the predicted feasibility of grayspace sensor networks, we study the deployment constraints of a hypothetical secondary network co-located with the TV broadcasting network of Germany. Our analysis shows that if we aim to support a minimum sensor-sensor distance, no universal coverage can be maintained in this country. While our quantitative results are specific to Germany, we deem them indicative for the expected results also in other potential deployments. We found that while a secondary wireless sensor network in TVGS is technically possible, the necessary constraints on operational parameters and service levels for TVGS co-existence will significantly limit its practical viability.
Abstract TP19: Thrombectomy in Medium Arteries Works for Distal Vessel Occlusions in Acute Ischemic Stroke - STRATIS (2020)

Background: Mechanical thrombectomy is established for large vessel occlusions in acute ischemic stroke, but the potential role in distal vessel occlusions of medium arteries is largely unknown. Such distal arterial segments have not been measured with respect to thrombectomy devices used during endovascular therapy. We conducted a systematic analysis of arterial size, segmental anatomy and stent retriever device performance during thrombectomy. Methods: The STRATIS angiography core lab adjudicated the exact location of the occlusion, proximal and distal device deployment, relationship to arterial bifurcations and anatomical nomenclature. Arterial diameters were measured at all of these sites. Statistical analyses examined the relationship between these variables, arterial recanalization and eTICI reperfusion. Results: Thrombectomy was performed with various device sizes, including Solitaire 4x40 in 36.3% (306/844), Solitaire 6x30 in 31.4% (265/844), Solitaire 4x20 in 26.4% (223/844), unspecified in 3.8% (32/844), Solitaire 6x20 in 1.3% (11/844) and Solitaire 4x15 in 0.8% (7/844). Arterial diameter at the occlusion site was median 2.17mm (1.40-3.59) in the distal M1, 1.67mm (0.81-2.98) in the proximal M2, 1.50mm (0.92-1.99) in the distal M2, 1.24mm (0.67-2.00) in the M3 and 1.88mm (1.49-1.94) in the P1. Considerable overlap was noted between arterial sizes at occlusion sites carrying different segmental arterial nomenclature or vessel names. During device deployment in STRATIS, median arterial diameter at the occlusion site was 2.4mm (IQR 1.9, 3.4), 2.9mm (IQR 2.2, 3.6) at the proximal stent marker and 1.4mm (IQR 1.2, 1.7) at the distal stent marker. Substantial eTICI reperfusion (2b-3) was achieved in all distal vessel occlusions (Table 1). Conclusions: Substantial reperfusion may be achieved with currently available mechanical thrombectomy devices for distal vessel occlusions in medium arteries.
Three-dimensional Rism Theory for Molecular Liquids and Solid-Liquid Interfaces (2006)

Peer reviewed: Yes
Interference channel with a relay: Models, relaying strategies, bounds (2009)

This paper discusses the impact of relaying in interference-limited networks by studying a two-user Gaussian interference channel with a relay (ICR). Various models for relay reception and transmission are possible: The relay can receive and transmit in the same band as the sources (i.e., in-band relay reception/transmission), or else relay reception, or both reception and transmission, can take place over orthogonal links of limited capacity (i.e., out-of-band relay reception or/ and transmission). In all scenarios, the selection of either signal relaying, interference forwarding or a combination thereof for the relay operation is identified as a common design choice. While signal relaying enables the destination to obtain a stronger desired signal or additional information, interference forwarding helps removing part of the interference. Important scenarios under which signal relaying and interference forwarding are optimal are identified, including cognitive relaying where the relay is unaware of the source codebooks and out-of band relaying, both under certain modified strong interference conditions and the latter under additional capacity constraints on the orthogonal relay links.
Beware of First Impressions (2008)

A 64-year-old Filipino man presented to a Baltimore hospital with a 4-month history of worsening midback pain, progressive leg weakness, and intermittent bladder and bowel incontinence. He had no fever or pulmonary symptoms. Magnetic resonance imaging (MRI) of the thoracic spine revealed hypointense T1-weighted and hyperintense T2-weighted bone marrow signal involving vertebral bodies T2, T3, and T4 (findings that were consistent with osteomyelitis); vertebral compression fractures; an epidural fluid collection; and spinal cord compression (Fig. 1). Multiple blood cultures were negative. Because the spine was considered unstable, he underwent T2, T3, and T4 vertebrectomy with fusion from C3 to T8. Pathological studies of the operative specimen revealed granulation and chronic inflammation. No organisms were identified with the use of routine or special stains, including an auramineâ phenol stain for acid-fast bacilli. Vertebral bone and material from the fluid collection were sent for fungal, mycobacterial, and routine bacterial cultures before the initiation of treatment with antimicrobial agents.
Combined Treatment of Heterocyclic Analogues and Benznidazole upon Trypanosoma cruzi In Vivo (2011)

Chagas disease caused by Trypanosoma cruzi is an important cause of mortality and morbidity in Latin America but no vaccines or safe chemotherapeutic agents are available. Combined therapy is envisioned as an ideal approach since it may enhance efficacy by acting upon different cellular targets, may reduce toxicity and minimize the risk of drug resistance. Therefore, we investigated the activity of benznidazole (Bz) in combination with the diamidine prodrug DB289 and in combination with the arylimidamide DB766 upon T. cruzi infection in vivo. The oral treatment of T.cruzi-infected mice with DB289 and Benznidazole (Bz) alone reduced the number of circulating parasites compared with untreated mice by about 70% and 90%, respectively. However, the combination of these two compounds decreased the parasitemia by 99% and protected against animal mortality by 100%, but without providing a parasitological cure. When Bz (p.o) was combined with DB766 (via i.p. route), at least a 99.5% decrease in parasitemia levels was observed. DB766+Bz also provided 100% protection against mice mortality while Bz alone provided about 87% protection. This combined therapy also reduced the tissular lesions induced by T. cruzi infection: Bz alone reduced GPT and CK plasma levels by about 12% and 78% compared to untreated mice group, the combination of Bz with DB766 resulted in a reduction of GPT and CK plasma levels of 56% and 91%. Cure assessment through hemocultive and PCR approaches showed that Bz did not provide a parasitological cure, however, DB766 alone or associated with Bz cured ≥13% of surviving animals.
WiMAX Network Automation: Neighbor Discovery, Capabilities Negotiation, Auto‐Configuration and Network Topology Learning (2009)

This chapter contains sections titled: Introduction WiMAX Network Elements Auto-discovery Automatic Learning of the WiMAX Network Topology Capabilities Exchange Automatic WiMAX Version Management Automated Roaming Conclusion: Network Automationas a WiMAX Differentiator References
LLLl lattice-basis reduction achieves the maximum diversity in MIMO systems (2005)

Diversity order is an important measure for the performance of different communication systems over MIMO fading channels. In this paper, we define the preceding diversity for the fixed-rate MIMO broadcast systems and we prove that in these systems, lattice-reduction-aided preceding achieves the preceding diversity. Also, we prove that lattice-reduction-aided decoding achieves the receive diversity in MIMO point-to-point and multiple-access systems
Comparative laser spectroscopic study of DNA and polynucleotide adducts from the (+)-anti-diol epoxide of benzo[a]pyrene (1991)

A recently developed methodology [Jankowiak, R., Lu, P., Small, G. J., and Geacintov, N. E. (1990) Chem. Res. Toxicol. 3, 39-46], which combines fluorescence line narrowing spectroscopy at 4.2 K with non-line-narrowed (S2----S0 laser excitation) fluorescence spectroscopy at 77 K and fluorescence quenching, is used to characterize adducts formed from (+)-anti-BPDE and the alternating copolymers poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT), the nonalternating poly (dG).poly(dC), single-strand poly(dG), and the oligonucleotide d(ATATGTATA). Detailed comparisons of the fluorescence spectra and quenching (with acrylamide) of the properties of the adducts with those of (+)-anti-BPDE-DNA adducts are made. Fluorescence spectra of the trans and cis isomers of the adduct formed from guanosine monophosphate and the adducts of d(ATATGTATA) are used to assign the stereochemistry of the two major DNA adducts as trans-N2-dG moieties which occupy two different DNA sites. Evidence for the existence of minor cis-type guanine adducts is provided. Finally, a fourth type of DNA adduct (minor) is identified and assigned as trans-N6-dA.
SU‐F‐I‐48: Variability in CT Scanning Over‐Range Across Clinical Operation (2016)

Purpose: Inconsistency in the scan range for a given protocol can be a source of variability in patient dose. The purpose of this study was to determine the variability in the over‐scan length in clinical CT operation for chest and abdominopelvic (A&amp;P) protocols. Methods: A total of 51 abdomen‐pelvis and 121 chest CT exams were randomly selected from our clinical database. A commercial dose monitoring solution was used to extract and database the total exposure area and the geometrical information related to automatically‐segmented anatomical landmarks for each target region. The data were exported off‐line for the statistical analysis. The over‐scan length (delta) was calculated as the difference between the real scanned length and ideal scanning length based on the anatomical landmarks for each target region. Results: The mean delta for abdomen‐pelvis exams was 12 mm (median 8 mm; min −191 mm; max 158 mm; standard deviation 71 mm). The average delta values at the interfaces with the chest and lower extremity regions were 69 mm and −57 mm, respectively. For chest exams, the average delta was 91 mm (median 93 mm; min 36 mm; max 190 mm; standard deviation 29 mm), and the average delta values at interfaces with the neck and abdomen regions were 26 mm and 65 mm, respectively. The percentage delta mean related to the abdomen‐pelvis and chest lengths were 3% and 45%, respectively. Conclusion: Although there is greater over‐scan in the chest region, there is considerably more variability in the over‐scan area for abdomen‐pelvis exams. Estimation of the over‐scan length must be included in the effective dose estimates, which uses different coefficients for different target region (ICRP 102). Furthermore, knowledge of over‐scan lengths and variability can guide steps to improve clinical consistency and operation.
Metabolomic Profiling of Long‐Term Weight Change: Role of Oxidative Stress and Urate Levels in Weight Gain (2017)

Metabolites linked to higher oxidative stress are associated with increased long-term weight gain.
Immobilization of Nanoscale Sunscreening Agents onto Natural Halloysite Micropowder (2015)

Titanium dioxide (TiO2) nanoparticles contained in sunscreen products are typically smaller than 30 nm in order to enhance the efficacy of the sun protection. TiO2 nanoparticles of this size range raise toxicity concerns because of the generation of reactive oxygen species (ROS) and the ability to penetrate into the skin tissue. To solve these problems, we immobilized the nanoparticles on a natural tubular powder, halloysite. The nanoparticle-halloysite hybrid powders are prepared by two synthetic methods: an ex situ immobilization of TiO2 nanoparticles (after separate synthesis of a nanoparticle batch), and an in situ generation of TiO2 nanoparticles inside halloysite. Notably, TiO2 nanoparticles of pure rutile phase are synthesized so that the ROS generation is suppressed before immobilization. The ultraviolet-visible (UV-vis) light extinction results show that the sunscreening efficacy of the hybrid powder produced via the ex situ route appears to be 22% higher than that of the hybrid powder fabricated by the in situ method. An increase in the hybrid powder concentration results in a sunscreening efficiency equivalent to that of the bare TiO2 nanoparticles. Our results can be used to produce nanoparticle-halloysite hybrid powders suitable for UV light screening while reducing the potential toxicity concerns.