cssi/SciSciGPT-SciSciNet huggingface dataset:
Metabolic Effects of Poly(ADP-Ribose) Inhibitors

3-Aminobenzamide (3-AB) and benzamide inhibit the synthesis of the biopolymer, poly(ADP-ribose), after exposure of cells to DNA- damaging agents [7]. Stimulation of poly(ADP-ribose) synthesis is believed to be necessary for normal DNA repair processes; its inhibition by 3-AB or benzamide delays ligation after excision of damaged DNA and repair synthesis at the site of excision [3, 5]. It has been proposed that 3-AB and benzamide alter poly(ADP-ribose) synthesis by specific inhibition of the enzyme poly(ADP-ribose) synthetase [6]. However, very little work has been done on the effects of 3-AB or benzamide on cellular metabolism; it has generally been assumed that they have no “profound metabolic effects of an unknown character in undamaged cells” [4].
Downregulation of pulmonary atrial natriuretic peptide receptors in rats exposed to chronic hypoxia

We hypothesized that a downregulation in pulmonary atrial natriuretic peptide (ANP) receptors helps raise plasma ANP levels during chronic hypoxia. We measured in vivo pulmonary uptake and plasma c...
Osobliwym gawędom nie ma końca (Adamowi Lipszycowi w odpowiedzi)

No end to weird narratives In his polemic with the author of ‘Powszechna rozwiązlośc: Schulz, egzystencja, literatura’, Adam Lipszyc defended a messianic interpretation of Schulz’s work, rejected by Markowski wholesale as based on insufficient textual evidence. According to Markowski all attempts at in scribing Schulz in the messianic tradition, no matter how defined, must fail because they do not acknowledge a parodic and ironic dimension of Schulz’s worldview, which ruins any serious access to religious thinking of which messianism is a clear example
PROLONGED ARTIFICIAL VENTILATION: A QUANTITATIVE APPROACH.

A special five bed unit for the care of patients requiring tracheostomy and prolonged artificial ventilation was established at the Massachusetts General Hospital in 1961. More than 300 patients have been treated in this unit. This experience is the background for a discussion of the complex problems of choosing the type and pattern of ventilation, insuring adequate oxygenation and carbon dioxide elimination, and preventing and treating complications.
Fluorescence lifetime imaging microscopy reveals quenching of fluorescein within corneal epithelium.

Topical application of fluorescein results in background fluorescence of normal corneal epithelial cells. The fluorescence appears relatively weak and is often ignored clinically. The concentrations of fluorescein applied clinically exceed the threshold for self quenching. The possibility that exuberant topical concentrations of fluorescein result in quenching of fluorescence in tears and normal corneal epithelium is explored. Fluorescence lifetime measurements are sensitive to quenching and are less vulnerable to inner filter effect than steady state measurements. The types of fluorescence lifetime quenching often report informative molecular interactions. Therefore, fluorescence lifetime confocal imaging was performed in solutions, tears and corneal epithelium removed by membrane cytology following applied fluorescein. Amplitude averaged fluorescence lifetimes (τamp) were measured with time resolved single photon counting using a pulsed diode laser for excitation of fluorescein. Lifetime decays were fit to multi-exponential models with least squares analysis. Stern-Volmer plots for both intensity (I) and (τamp) were determined. Stern-Volmer plots demonstrated both dynamic and static quenching components (R(2) = 0.98 exponential fit, I0/I). Plots of τamp versus concentration of fluorescein revealed a linear relationship. Immediately after fluorescein application, quenching was evident in tears (τamp < 1 ns) versus tears sampled after 5 min (τamp = 3.7 ns). Corneal epithelium showed quenching (τamp ≤ 2 ns) from 1 to 16 min post fluorescein instillation. Clinical concentrations of fluorescein show self-quenching but rapidly dilute as tears turnover. Intracellular quenching occurs in normal corneal epithelium. Lifetime decay curves suggest complex mechanisms are involved. Quenching is a plausible explanation for the low fluorescence background observed clinically.
Another Evidence Shows Cultural Relationship Between America and China

American Spiro Cultureis is one of ancient American culture. Quite a lot of its engraving signs,cultural relics and engraving vein decoration are similar to those in China. Therefore, we deduce that there is a possible direct or indirect relationship between Spiro Culture and Chinese Culture.
Cost Considerations in Therapy with Myeloid Growth Factors

Costs of biologic response modifiers, specifically myeloid growth factors, are discussed relative to cost offsets they may produce in the total amount spent on health care in patients with certain disease states. Even though the biologic response modifiers granulocyte colony-stimulating factor (filgrastim) and granulocyte-macrophage colony-stimulating factor (sargramostim or molgramostim) are similar in name, they are chemically and biologically different. These differences result in different clinical applications. Administered after myelosuppressive antineoplastic therapy, filgrastim decreases the risk of infection. The growth factors may also be useful in patients undergoing bone marrow transplantation, in nonneutropenic patients with bacterial infections, and in patients with other disease states. Although the myeloid growth factors are somewhat expensive in terms of acquisition cost, their use is usually associated with a decrease in the risk of medical complications requiring health care expenditures, often for hospitalizations or antimicrobials. The precise cost of acquiring and administering myeloid growth factors depends on three interdependent variables: the factor used, the dosage of the drug, and the duration of therapy. Cost offsets may be more difficult to define, but they would include direct cost offsets, such as reduced episodes of febrile neutropenia and fewer, less-intense days of hospitalization or treatment. Sargramostim and molgramostim have demonstrated efficacy when given after bone marrow transplantation; filgrastim has been shown to lower infection rates by at least 50% after myelosuppressive antineoplastic therapy and in patients with severe chronic neutropenia.(ABSTRACT TRUNCATED AT 250 WORDS)
Androgen-Responsive Functions of Male Rat Liver Effect of Chronic Alcohol Ingestion

Many liver processes are sexually dimorphic, and in rats, testosterone is the major steroid hormone determinant of the differing patterns of hepatic function. The microsomal content of specific enzymes and the syntheses of specific proteins are dependent on serum testosterone to maintain this dimorphism. Because the liver of male rats is strikingly androgen responsive, and because chronic alcohol ingestion decreases serum testosterone, we sought to determine whether chronic alcohol feeding would alter the masculine pattern of hepatic liver function in male rats. We quantitated both the cytosolic and nuclear forms of the hepatic androgen receptor. Alcohol feeding of male rats results in a significant loss of both types of androgen receptor sites; the specific binding capacity of both cytosolic and nuclear receptor in alcohol-fed rats is reduced to about 30% of that in either isocalorically fed rats or rats fed ad libitum. This reduction in hepatic androgen receptor activity is concomitant with a 50% reduction in serum testosterone content in the alcohol-fed animals. In addition, the activities of two hepatic androgen-responsive proteins, namely a cytosolic estrogen binder and a microsomal enzyme, estrogen 2-hydroxylase, demonstrate a decrease in activity that parallels the decreases in both forms of the androgen receptor. Administration of testosterone to the alcohol-fed animals normalized both the hepatic androgen receptor and the androgen-responsive protein activities. From these results, we conclude that chronic alcohol feeding results in a decreased androgen responsiveness of the liver, a condition that most likely results from the decreased serum testosterone levels in the alcohol-fed animals.
Heterotransplantation of human multiple myeloma cell lines in severe combined immunodeficiency (SCID) mice

Human multiple myeloma (MM) xenografts have been difficult to establish in athymic mice. We examined the feasibility of establishing human MM xenograft growth in SCID mice following subcutaneous (sc) injection of 1-2 x 10(7) cells from the human plasma cell dyscrasia (PCD) cell lines RPMI 8226 and ARH-77. SC tumors emerged in 67% (6/9) of RPMI 8226- and 6 of 6 ARH-77-injected mice after a latency period of 9-54 days, and reached 19-35 mm in diameter before the mice were sacrificed. RPMI 8226 and ARH-77 primary tumor DNA hybridized positively with the human genome probe Alul-(Blur8), confirming successful engraftment of the human MM cell lines. The RPMI 8226 xenografts comprised predominantly of plasmacytoid cells that expressed the relevant cytoplasmic immunoglobulin (cIg) light chain isotype. Xenografted RPMI 8226 cells also expressed CD10 (CALLA; 44% reactive cells), CD38 (OKTIO; 69%), CD5 (49%), and reacted with the MM monoclonal antibody MM4 (39%). Human MM growth appeared to be localized subcutaneously for both RPMI 8226 and ARH-77 xenografts. There were no detectable metastatic foci in kidney, brain, heart, or bone marrow. Whereas diffuse plasma cell infiltrates were observed in spleen, GI tract, and lung biopsies of tumor-bearing mice, these infiltrates were of host origin according to immunophenotyping and DNA analyses. Neither the originating RPMI 8226 line nor its SCID mouse xenograft expressed Epstein Barr virus (EBV) genome sequences. These observations indicate that both EBV- (RPMI 8226) and EBV+ (ARH-77) cell lines can be successfully propagated in SCID mice.(ABSTRACT TRUNCATED AT 250 WORDS)
Lung transplantation in patients who have undergone prior cardiothoracic procedures

Background Patients who have undergone prior cardiothoracic procedures offer technical challenges that may affect post-transplant outcomes and be a reason to decline listing. Data are currently limited regarding the indication for lung transplantation among recipients who have had prior cardiothoracic procedures. Methods Of 453 lung transplants performed at Cleveland Clinic from January 2005 to July 2010, 206 recipients (45%) had undergone prior cardiothoracic procedures: 157 lung only, 15 cardiac only, 10 cardiac + lung, 10 pleurodesis + lung, and 14 other. Chest tube placement was performed in 202 patients. Survival, post-transplant length of intensive care unit and hospital stays, primary graft dysfunction, and pulmonary function outcomes were compared with outcomes of patients not having prior procedures using propensity score adjustment. Results Short-term and long-term survival was similar between the 2 groups. Survival at 30 days, 1 year, and 5 years was 94%, 83%, and 55% for the prior cardiothoracic procedure group and 96%, 84%, and 53% for the no prior cardiothoracic procedure group (log-rank p = 0.9). Intensive care unit stay was longer (6 days vs 5 days, p = 0.02) in the prior cardiothoracic procedure group; this was particularly true for pleurodesis + lung (10 days, p = 0.05), although post-transplant hospital stay was similar (16 days, 16 days, and 22 days; p = 0.13). Primary graft dysfunction was not increased in the prior cardiothoracic procedure group. Forced expiratory volume in 1 second was similar for both groups but lower for thoracotomy and lung procedures using a bilateral chest tube ( p Conclusions A prior cardiothoracic procedure is not a contraindication for lung transplantation.
Towards A Complete Species Level Phylogeny of Leptosiphon (Polemoniaceae)

Abstract Leptosiphon Benth. (Polemoniaceae) has 40 taxa, distributed mainly in western North America, with one species in Chile. Phylogenetic studies of Polemoniaceae have consistently supported recognition of Leptosiphon as a separate genus from Linanthus, and resolved an array of taxonomic problems; however, several issues remained unclear for Leptosiphon. In those studies, sampling of Leptosiphon was incomplete, and certain species having strikingly similar floral morphologies appeared non-monophyletic, while other species groups with divergent floral morphologies formed a clade. Our analyses use greater sampling across taxa in Leptosiphon and, in addition to nrITS, the non-coding chloroplast region trnS–trnG to help resolve the genus phylogeny. These results yielded a more complete phylogeny from which to base further research on floral evolution in this group. However, much work remains to be done in resolving species level relationships. Analyses of morphological character evolution suggest that sev...
Long-term outcomes of stereotactic body radiation therapy (SBRT) with fiducial tracking for inoperable stage I non-small cell lung cancer (NSCLC)

Stereotactic body radiation therapy (SBRT) for stage I non-small cell lung cancer (NSCLC) is considered standard of care in the medically inoperable patient population. Multiple methods of SBRT delivery exist including fiducial-based tumor tracking, which allows for smaller treatment margins and avoidance of patient immobilization devices. We explore the long-term clinical outcomes of this novel fiducial-based SBRT method. In this single institutional retrospective review, we detail the outcomes of medically inoperable pathologically confirmed stage I NSCLC. Patients were treated with the Cyberknife SBRT system using a planning target volume (PTV) defined as a 5-mm expansion from gross tumor volume (GTV) without creation of an internal target volume (ITV). Dose was delivered in three or five equal fractions of 10 to 20 Gy. Pretreatment and posttreatment pulmonary function test (PFT) changes and evidence of late radiological rib fractures were analyzed for the majority of patients. Actuarial local control, locoregional control, distant control, and overall survival were calculated using the Kaplan-Meier method. Sixty-one patients with a median age of 75 years were available for analysis. The majority (80 %) of patients were deemed to be medically inoperable due to underlying pulmonary dysfunction. Eleven patients (18 %) developed symptomatic pneumothoraces secondary to fiducial placement under CT guidance, which precipitously dropped to 0 % following transition to bronchoscopic fiducial placement. The 2-year rib fracture risk was 21.4 % with a median time to rib fracture of 2.9 years. PFTs averaged over all patients and parameters demonstrated small absolute declines, 5.7 % averaged PFT decline, at approximately 1 year of follow-up, but only the diffusing capacity of lung for carbon monoxide (DLCO) demonstrated a statistically significant decline (10.29 vs. 9.01 mL/min/mmHg, p = 0.01). Five-year local control, locoregional control, and overall survival were 87.6, 71.8, and 39.3 %, respectively. Despite reduced treatment margins and lack of patient immobilization, SBRT with fiducial-based tumor tracking achieves clinically comparable long-term outcomes to other linac-based SBRT approaches.
Gendered Labour, Migratory Labour: Reforming Sugar Regimes in Xinavane, Mozambique

Sugar has played a contentious historical role in the development of Mozambique. Following the country’s 16-year civil conflict, the industry has re-emerged as an important sector for investment and national rebuilding. This article explores how the industry’s narratives of technical efficiency and success in increasing production mask dynamics of agricultural labour in the country’s largest sugar estate at Xinavane, southern Mozambique. Based on archival and ethnographic investigation, the paper interrogates the recent transformation of sugar cane production by South African investment and management. The paper identifies gender- and migration-based labour management practices that are not only consistent with a trend toward labour ‘flexibilisation’ within South African agribusiness practice, but also constitute rules and orders that reiterate Portuguese colonial practice. This analysis undermines current ahistorical narratives of the Acucareira de Xinavane – or Xinavane Sugar Mill – that depict the comp...
Decoding by iterative detection (DECIDET): Soft-in/soft-out decoding of arbitrary linear block codes over arbitrary finite fields

This paper presents a framework for an error correction decoding algorithm which can perform soft-input/soft-output decoding on arbitrary linear block codes over arbitrary finite fields. The algorithm produces estimates of individual symbols by detecting the symbol as a scalar multiple of a column of the generator matrix for the code, with other columns forming an interfering “noise” which is probabilistically modeled. Only the generator matrix is used for the decoder; the parity check matrix is not employed. The posterior probability so obtained is iteratively fed back as a prior input for turbo-like operation. Methods of incorporating statistical dependence among symbols are presented. The decoder can be used for channels with arbitrary noise distributions. Computation over larger fields is achieved through the use of an extended Hadamard transform, which is used to compute the distribution of arbitrary linear combinations of random variables distributed over the field. Results are presented for some codes of various lengths and design distances.
Gauging AWE staff

Your news story about the latest developments at the UK's Atomic Weapons Establishment (AWE) in Aldermaston included a patronizing comment from a member of the British Pugwash Group (October pp8–9). He said that if AWE became more open, then "a wider community of outsiders would be able to gauge the quality of AWE's staff through interactions in open science".
The Impacts of Domain-General vs. Domain-Specific Diagramming Tools on Writing

Argument diagramming is the process of spatially representing an argument by its component parts and their relationships. A growing body of evidence supports the use of argument diagramming to aid student learning and writing within disciplines including science education. However, most of these studies have focused on basic contrasts between diagramming and no diagramming. The purpose of this study was to learn how different diagramming frameworks affect the benefits afforded by argument diagramming. Three groups of undergraduate students in psychology research methods lab courses were given either no diagramming support, support with a domain-general framework, or support with a domain-specific framework to help them write a research paper introduction. Students given any diagramming support included more relevant citations and considered opposing citations in their papers. Students using the domain-specific framework wrote more about the scientific validity of cited studies than the other two groups, whereas students using the domain-general framework trended towards included more supporting citations.
Epidermal Growth Factor Is an Independent Prognostic Factor in Patients with Chronic Lymphocytic Leukemia.

Abstract Epidermal growth factor (EGF) is a polypeptide expressed in various epithelial tissues and organs. EGF is believed to play an important role in cell development, differentiation, growth, apoptosis, and epithelial regeneration by the activation of signal transduction pathways that include PI3K/AKT, RAS/ERK, and JAK/STAT. These pathways may lead to both pro- and anti-apoptotic proteins. While hematopoietic cells do not express a significant amount of the EGF receptor (EGFR), bone marrow stromal cell and fibroblast expression of EGFR and EGF is important in the support of mesenchymal stem cell growth and colony formation. Since stromal cells play a major role in hematologic diseases, we evaluated the level of EGF in the plasma of 120 patients with chronic lymphocytic leukemia (CLL). EGF levels were significantly lower in CLL patients (median, 86.7; range, 2.2–500 pg/mL) than in 22 normal controls (median, 151.7; range, 35.1–389.1 pg/mL) (P = 0.02). EGF levels did not correlate significantly with β2-microglobulin (β2-M) level or IgVH mutation status, but correlated negatively with Rai stage (P = 0.0001). EGF level correlated positively with platelet count (R = 0.53, P Download : Download high-res image (74KB) Download : Download full-size image
Prediction of 6-minute walk performance in patients with peripheral artery disease

Abstract Background Peripheral artery disease (PAD) is a highly prevalent disease that impairs walking ability. Walking tests, such as the 6-minute walk test (6MWT) and 4-meter walk test, are commonly used to assess exercise endurance and ambulatory function over a short distance, respectively. The 6MWT performance is predictive of PAD severity and disease outcomes, but it is not feasible in many clinical settings because it requires a long walkway to serve as the test route and lengthens clinic visits. As an alternative, the 4-meter walk test is convenient, inexpensive, and repeatable, but whether it accurately predicts endurance performance in the long-distance 6MWT is not known. The goal of this study was to develop a statistical model to predict 6MWT gait speed from 4-meter walk test results and clinical characteristics among patients with PAD. Methods Measures of 6MWT gait speed were derived from 183 patients with symptomatic PAD who were evaluated at the University of Oklahoma Health Sciences Center (2004-2012). The testing procedures and research personnel remained constant throughout the duration of the study. Independent variables included demographic and clinical information and 4-meter walk test gait speed. Fivefold cross validation and manual backward selection were used for model selection. Adjusted R 2 and corrected Akaike information criterion were applied to quantify the predictive performance of the regression models. Results A total of 183 people (54% male; mean age, 65 [standard deviation (SD), 10] years) with moderate PAD severity (ankle-brachial index [ABI]; mean, 0.72 [SD, 0.24]) performed the walking tests. Participants covered an average distance of 335 (SD, 97) m distance in the 6MWT. The 4-meter walk gait speed, ABI, and dyspnea were independent predictors of 6MWT speed in the multivariate model (adjusted R 2 = 0.55). The model resulted in 95% prediction interval widths of 30 m for mean and 260 m for individual predicted 6MWT distance measures. Conclusions Slower 4-meter walking speed, lower ABI, and presence of dyspnea all predict slower 6MWT gait speed, which corresponds to shorter 6MWT distance. Prediction of group means is reasonably precise; however, prediction of individual patient 6MWT performance is imprecise relative to between-group differences that are clinically important.
Twinning-mediated work hardening and texture evolution in CrCoFeMnNi high entropy alloys at cryogenic temperature

Abstract The cryogenic plastic deformation of CrCoFeMnNi high entropy alloy is characterized by three distinct stages based on the change of the work hardening rate. Microstructure and bulk texture at different strain levels were studied by electron backscatter diffraction (EBSD) and neutron diffraction. Our findings indicate that the deformation twins led to the constant work hardening rate at Stage II and resulted in the appearance of 〈115〉//TA texture component, while the dislocation slip was involved all though the entire plastic deformation. The twinning-mediated tensile plastic deformation at cryogenic temperature finally induced the strong {111}-〈112〉 texture component and minor {001}〈110〉 texture component accompanied with twinning-induced {115}〈552〉 texture component.
Improving reliability of weak PUFs via circuit techniques to enhance mismatch

In recent years, SRAM-based and other Weak PUFs have found applications in tamper sensitive key storage and ID generation. SRAM-based PUFs, for example, rely on intrinsic process variations to enable repeatable and unique start-up behavior of their outputs. However, noise in the system can compromise repeatability of SRAM start-up behavior. To obviate this problem, a number of solutions such as fuzzy extraction and error correcting codes have been proposed to generate a stable key from PUF cells. However, these methods require a large number of initial PUF bits. In this work, we discuss circuit techniques that create new Weak PUFs by modifying the cross-coupled elements of a traditional storage cell to amplify the impact of process variations and create a higher degree of mismatch. With increased mismatch, the intrinsic error rates of the new PUF cells decrease, thereby reducing the number of PUF cells and amount of auxiliary circuitry needed for fuzzy extraction or ECC. Our results show that the new designs give 4x to 9x reduction in error rates compared to a standard cross-coupled inverter design. We also highlight the area savings that can be achieved in hardware implementations of ECC systems due to improving the inherent reliability of the PUF cells.
Thalamic Models of Seizures In Vitro

Abstract The thalamus is a subcortical structure that mediates attention, perception, consciousness, and rhythm generation (Jones, E.G., 1985. The Thalamus. Springer Science + Business Media, LLC, New York, NY, pp. 935). The rhythmogenic properties of the thalamus, with extensive, reciprocal connections with the cortex, emerge from the thalamocortical and intrathalamic circuits. Disruptions in these properties, or maladaptive rhythmogenesis, underlie seizures and epilepsy. This chapter will highlight how in vitro slice physiology can be used to model thalamic rhythmogenic properties, and their contribution to different subtypes of epilepsies, such as idiopathic generalized epilepsies or acquired epilepsies, and to investigate potential mechanisms that influence thalamic involvement in epileptogenesis, such as glial-neuronal interactions. It will also demonstrate how slice physiology can be combined with cutting-edge tools, such as optogenetics, to support more precise manipulation and mapping of thalamic circuits.
A novel iris transillumination grading scale allowing flexible assessment with quantitative image analysis and visual matching.

ABSTRACTPurpose: To develop a sensitive scale of iris transillumination suitable for clinical and research use, with the capability of either quantitative analysis or visual matching of images.Methods: Iris transillumination photographic images were used from 70 study subjects with ocular or oculocutaneous albinism. Subjects represented a broad range of ocular pigmentation. A subset of images was subjected to image analysis and ranking by both expert and nonexpert reviewers. Quantitative ordering of images was compared with ordering by visual inspection. Images were binned to establish an 8-point scale. Ranking consistency was evaluated using the Kendall rank correlation coefficient (Kendall’s tau). Visual ranking results were assessed using Kendall’s coefficient of concordance (Kendall’s W) analysis.Results: There was a high degree of correlation among the image analysis, expert-based and non-expert-based image rankings. Pairwise comparisons of the quantitative ranking with each reviewer generated an ave...
Human Papillomavirus Vaccination: What Are the Reasons for Nonvaccination Among U.S. Adolescents?

Abstract Purpose Human papillomavirus (HPV) vaccination is recommended for 11- to 12-year-old U.S. adolescents. Unfortunately, HPV vaccine rates have been suboptimal. Parents are key decision agents regarding their adolescents' health; thus, it is necessary to understand their reasons for not vaccinating their adolescents. The purpose of this study was to compare parents' primary reasons for non-HPV vaccination by calendar year, sex of the child, and level of vaccine hesitancy. Methods The National Immunization Survey-Teen 2012–2015 was subset to parents who did not intend for their adolescent to receive the HPV vaccine in the next 12 months (N = 59,897). Survey-weighted logistic regression models assessed the impact of year, sex, and level of hesitancy on main reasons for nonvaccination. Results Not receiving a recommendation and lack of knowledge were significantly more likely to be the reasons for nonvaccination in 2012 and 2013 compared with 2015. The following reasons were significantly less likely to be reported for females compared with males: not recommended (odds ratio [OR] = .63, 95% confidence interval [CI], .58–.69) and lack of knowledge (OR = .86, 95% CI, .79–.94). In contrast, parents of females were more likely to state they were concerned about safety and side effects (OR = 2.19, 95% CI, 1.98–2.41). Differences in reasons for nonvaccination were observed between those who were unlikely and unsure regarding receiving the HPV vaccine. Conclusions Findings indicate that U.S. parental attitudes about HPV vaccination have changed over time and reasons for nonvaccination vary based on the sex of the adolescent and the level of hesitancy of the parent. This information can shape how providers respond to parental concerns and HPV vaccine hesitancy.
Proteomics Insights into Autophagy

Autophagy, a conserved cellular process by which cells recycle their contents either to maintain basal homeostasis or in response to external stimuli, has for the past two decades become one of the most studied physiological processes in cell biology. The 2016 Nobel Prize in Medicine and Biology awarded to Dr. Ohsumi Yoshinori, one of the first scientists to characterize this cellular mechanism, attests to its importance. The induction and consequent completion of the process of autophagy results in wide ranging changes to the cellular proteome as well as the secretome. MS-based proteomics affords the ability to measure, in an unbiased manner, the ubiquitous changes that occur when autophagy is initiated and progresses in the cell. The continuous improvements and advances in mass spectrometers, especially relating to ionization sources and detectors, coupled with advances in proteomics experimental design, has made it possible to study autophagy, among other process, in great detail. Innovative labeling strategies and protein separation techniques as well as complementary methods including immuno-capture/blotting/staining have been used in proteomics studies to provide more specific protein identification. In this review, we will discuss recent advances in proteomics studies focused on autophagy.
Mechanical properties of resin-based cements with different dispensing and mixing methods.

Abstract Statement of problem Resin-based cements are frequently used in clinical practice. To reduce time and technique sensitivity, manufacturers have introduced the same brand of cement with different dispensing methods. The effect of this change on properties of the cement is unknown. Purpose The purpose of this in vitro study was to evaluate the mechanical properties of resin-based cements with different dispensing systems. Material and methods Specimens of resin-based cements (n=14) PANAVIA SA Cement Plus Handmix, PANAVIA SA Cement Plus Automix, RelyX Unicem Handmix, RelyX Unicem 2 Automix, G-CEM Capsule Automix, G-CEM LinkAce Automix, Variolink II Handmix, and Variolink Esthetic Automix were prepared for each mechanical test. They were examined after thermocycling (n=7/subgroup) for 20 000 cycles as to fracture toughness (FT) (ISO standard 6872; single-edge V-notched beam method), compressive strength (CS) (ISO 9917-1), and diametral tensile strength (DTS). The specimens were mounted and loaded at a crosshead rate of 1 mm/min (0.5 mm/min for FT) with a universal testing machine until failure occurred. The 2-and 1-way ANOVA followed by the Tukey HSD post hoc test were used to analyze data for statistical significance (α=05). Results Thermocycling had a significant effect in reducing the FT property of all resin-based cements except RelyX Unicem 2 and G-CEM LinkAce (P Conclusions Changing the dispensing method alters the mechanical properties of resin-based cements. The clinical significance of these results is yet to be determined.
DNA Implementation of Fuzzy Inference Engine: Towards DNA Decision-Making Systems

Decision-making systems are an integral part of any autonomous device. With the recent developments in bio-nanorobots, smart drugs, and engineered viruses, there is an immediate need of decision-making systems which are bio-compatible in nature. DNA is considered a perfect candidate for designing the computing systems in such decision-making systems because of their bio-compatibility and programmability. Complex biological systems can be easily modeled/controlled using fuzzy logic operations with the help of linguistic rules. In this paper, we propose an enzyme-free DNA strand displacement-based architecture of fuzzy inference engine using the fuzzy operators, such as fuzzy intersection and union. The basic building blocks of this architecture are minimum, maximum, and fan-out gates. All these gates are analog in nature, which means that the input/output values of the gates are represented by the concentration of the input/output DNA strands. To demonstrate the performance of the proposed architecture, a detailed design, analysis, and kinetic simulation of each gate were carried out. Finally, the minimum and maximum gates are cascaded according to the pre-defined rules to design the fuzzy inference engine. All these DNA circuits are implemented and simulated in Visual DSD software.
Routing protocol design in tag-to-tag networks with capability-enhanced passive tags

Radio frequency identification (RFID) is a technology that incorporates the use of electromagnetic fields to uniquely identity objects. Among different types of RFID tags, passive tags have some salient features such as light weight, low cost, small size, etc. However, the downside of passive RFID systems is very limited reading range due to lacking their own energy sources (passive RFID tags communicate solely by backscattering the reader's power). A novel concept of passive RFID tag-to-tag (T2T) communication has been recently proposed, via which passive tags in proximity (at centimeter level) can directly communicate with each other with the existence of an external energy source. Utilizing this concept, we proposed a Network of Tags (NeTa) that passive tags can connect with each other through multiple hops, using a the novel concept of turbo backscattering operation. This significantly enhances the scalability of such a T2T network. However, to implement the proposed NeTa architecture, one of the main issues is the inter-tag interference, which brings challenge to the routing protocol design. In our previous work [1], we introduced protocol design for both tag-to-reader routing and tag-to-tag routing, considering basic hardware capability of tags, i.e., tags cannot measure the strength of received signals. In this paper, we extend upon the results in [1] and focus on tag-to-tag routing for two distinct types of tags with different hardware capabilities — tags can measure and attenuate the received signal before backscattering. These functions can greatly reduce the inter-tag interference and therefore enhance the network throughput. The protocol design is based on solutions of two mixed integer nonlinear programming (MINLP) problems, respectively. The performances of the proposed protocols are analyzed and the impacts of several network factors (e.g., tag density, the transmit power of the reader, etc.) are investigated.
Cause and consequence of Aβ - Lipid interactions in Alzheimer disease pathogenesis.

Abstract Self-templating propagation of protein aggregate conformations is increasingly becoming a significant factor in many neurological diseases. In Alzheimer disease (AD), intrinsically disordered amyloid-β (Aβ) peptides undergo aggregation that is sensitive to environmental conditions. High-molecular weight aggregates of Aβ that form insoluble fibrils are deposited as senile plaques in AD brains. However, low-molecular weight aggregates called soluble oligomers are known to be the primary toxic agents responsible for neuronal dysfunction. The aggregation process is highly stochastic involving both homotypic (Aβ-Aβ) and heterotypic (Aβ with interacting partners) interactions. Two of the important members of interacting partners are membrane lipids and surfactants, to which Aβ shows a perpetual association. Aβ–membrane interactions have been widely investigated for more than two decades, and this research has provided a wealth of information. Although this has greatly enriched our understanding, the objective of this review is to consolidate the information from the literature that collectively showcases the unique phenomenon of lipid-mediated Aβ oligomer generation, which has largely remained inconspicuous. This is especially important because Aβ aggregate “strains” are increasingly becoming relevant in light of the correlations between the structure of aggregates and AD phenotypes. Here, we will focus on aspects of Aβ-lipid interactions specifically from the context of how lipid modulation generates a wide variety of biophysically and biochemically distinct oligomer sub-types. This, we believe, will refocus our thinking on the influence of lipids and open new approaches in delineating the mechanisms of AD pathogenesis. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
MICRO-METASTASIS OF BREAST CARCINOMA INTO THE ATRIAL MYXOMA

Primary cardiac tumors are extremely rare and we are presenting a case of an atrial myxoma with micro metastasis of breast carcinoma into the myxoma. A 55-year-old female presented with worsening shortness of breath with minimal exertion and significant lower back pain. Her vital signs were within
Outcomes of Glaucoma Drainage Device Surgery in Eyes with Treated Uveal Melanoma.

Aim We report patient safety and intraocular pressure (IOP) control after placement of a glaucoma drainage device (GDD) in eyes with a history of treated malignant uveal melanoma. Methods A retrospective review of the records of patients with uveal melanoma was performed. Outcomes were local tumor recurrence, rate of metastases, and to-nometric success, based on survival curves, defined as IOP < 21 mm Hg. Results Eleven eyes with choroidal melanoma, 4 with iris melanoma, and 1 with ciliary body melanoma were followed for a median (interquartile range) of 2.1 (1.1-3.2) years. Two subjects developed liver metastases; one had monosomy 3 and tumor gene expression profile class 2. The other case with ciliary body melanoma was negative for monosomy 3. There were no cases of local treatment failure. Mean preoperative IOP decreased from 30.5 ± 7.7 to 15.9 ± 8.1 mm Hg at 1 year after surgery (1-year success rate 80%). Conclusions Our case series with a median follow-up of 2 years shows that placing a GDD in patients with treated uveal melanoma does not expose patients to greater risk of local or extraocular recurrence. A larger series and longer follow-up time are required to fully evaluate the safety of GDDs in this clinical scenario.
Induction of Secondary Metabolite-Phytoalexin Formation in Plant Cell Suspension Cultures

Plants have the capability to synthesize a great variety of natural products. In general, compounds of interest have physiological and antimicrobial activity but were thought to be inert in the cells of origin and were therefore called secondary metabolites. More recently secondary natural products have been implicated in the defense response of plants against phytopathogens and were called phytoalexins. Besides having promise in the genetic development of disease resistant plant varieties, secondary products and their formation in plant cells suspension cultures has been of considerable interest. Plant cell suspension cultures which are high producers of the desired secondary metabolite would be an excellent model system to study biosynthetic and regulatory mechanisms. Although, growing plant cells in suspensions is not difficult, to stimulate these cells to produce the desired secondary metabolite in quantities sufficient for experimentation is considerably more difficult. Therefore, utilizing the stress or defense mechanism in plant cells could be beneficial in stimulation of plant cells to synthesize secondary natural products. We report here our efforts in elucidating the biochemical mechanism(s) of the induction of secondary metabolite formation.
Anticipatory Mobility Management by Big Data Analytics for Ultra-Low Latency Mobile Networking

Massive deployment of autonomous vehicles, un- manned aerial vehicles, and robots, brings in a new technology challenge to establish ultra-low end-to-end latency mobile networking to enable holistic computing mechanisms. With the aid of open-loop wireless communication and proactive network association in vehicle-centric heterogeneous network architecture, anticipatory mobility management relying on inference and learning from big vehicular data plays a key role to facilitate such a new technological paradigm. Anticipatory mobility management aims to predict APs to be connected in the next time instant and in a real-time manner, such that ultra-low latency downlink open-loop communication can be realized with proactive network association. In this paper, we successfully respond this technology challenge using big data analytics with location-based learning and inference tech- niques, to achieve satisfactory performance of predicting APs. Real vehicular movement data have been used to verify that the proposed prediction methods are effective for the purpose of anticipatory mobility management and thus ultra-low latency mobile networking.
Monozygotic twins diagnosed simultaneously with RAM immunophenotype acute myeloid leukemia.

AML with the RAM immunophenotype is associated with extremely poor prognosis. We report a rare case of monozygotic twins presenting simultaneously at the age of 2 years with RAM AML. Each twin underwent a myeloablative 7/10 unrelated umbilical cord blood transplant. Pretransplant Twin A's bone marrow was negative for MRD by flow cytometry (<0.01%) unlike Twin B's bone marrow (0.07%). Twin A is alive in remission 3 years from transplant. Twin B developed primary graft failure, but subsequently rescued with a haploidentical stem cell transplant. However, she relapsed and died 13 months from diagnosis. The twins' clinical courses demonstrate that upfront intensive chemotherapy to achieve negative MRD, followed by allogeneic hematopoietic stem cell transplant as postremission intensification strategy, should be considered in this high-risk AML.
Antimicrobial peptide similarity and classification through rough set theory using physicochemical boundaries

Antimicrobial peptides attract considerable interest as novel agents to combat infections. Their long-time potency across bacteria, viruses and fungi as part of diverse innate immune systems offers a solution to overcome the rising concerns from antibiotic resistance. With the rapid increase of antimicrobial peptides reported in the databases, peptide selection becomes a challenge. We propose similarity analyses to describe key properties that distinguish between active and non-active peptide sequences building upon the physicochemical properties of antimicrobial peptides. We used an iterative supervised machine learning approach to classify active peptides from inactive peptides with low false discovery rates in a relatively short computational search time. By generating explicit boundaries, our method defines new categories of active and inactive peptides based on their physicochemical properties. Consequently, it describes physicochemical characteristics of similarity among active peptides and the physicochemical boundaries between active and inactive peptides in a single process. To build the similarity boundaries, we used the rough set theory approach; to our knowledge, this is the first time that this approach has been used to classify peptides. The modified rough set theory method limits the number of values describing a boundary to a user-defined limit. Our method is optimized for specificity over selectivity. Noting that false positives increase activity assays while false negatives only increase computational search time, our method provided a low false discovery rate. Published datasets were used to compare our rough set theory method to other published classification methods and based on this comparison, we achieved high selectivity and comparable sensitivity to currently available methods. We developed rule sets that define physicochemical boundaries which allow us to directly classify the active sequences from inactive peptides. Existing classification methods are either sequence-order insensitive or length-dependent, whereas our method generates the rule sets that combine order-sensitive descriptors with length-independent descriptors. The method provides comparable or improved performance to currently available methods. Discovering the boundaries of physicochemical properties may lead to a new understanding of peptide similarity.
Risk and Protective Factors Related to Early Adverse Life Events in Irritable Bowel Syndrome.

BACKGROUND Irritable bowel syndrome (IBS) is a stress-sensitive disorder of brain-gut interactions associated with a higher prevalence of early adverse life events (EALs). However, it is incompletely understood how trauma severity or disclosure influence the risk of developing IBS or symptom severity. AIMS To determine whether (1) IBS patients report a greater number of EALs compared with healthy controls; (2) trauma severity and first age of EAL increase the odds of IBS; (3) confiding in others reduces the odds of IBS; (4) the number, trauma severity, and first age of EAL are associated with symptom severity; (5) sex differences exist. METHODS In total, 197 IBS patients (72% women, mean age=30.28 y) and 165 healthy controls (59% women, mean age=30.77 y) completed the Childhood Traumatic Events Scale, measuring severity of EALs and degree of confiding in others. Regression analyses were used to predict IBS status from EALs and association between gastrointestinal symptoms and EALs. RESULTS A greater number of EALs [odds ratio (OR)=1.36, 95% confidence interval (CI), 1.14-1.62; P<0.001] and higher perceived trauma severity (OR=1.13, 95% CI, 1.08-1.19; P<0.001) were associated with increased odds of IBS. Confiding in others decreased the odds of having IBS (OR=0.83, 95% CI, 0.72-0.96; P=0.012). The first age of EAL was not predictive of IBS. No sex differences were found. CONCLUSIONS Assessing the traumatic severity of EALs and amount of confiding in others is important as they can affect the risk of having IBS. Our findings emphasize early intervention to improve health outcomes in individuals with EALs.
Cost Saving Optimization Model for Energy Management System of a DC Microgrid Under Real Time Pricing

Microgrids are transforming the traditional way of meeting energy demands at several communities and establishments. They offer new avenues to achieve a carbon free, reliable, and resilient electric grid. With the advancements made in the power electronic converter technology, the DC microgrids are gaining popularity nowadays. This paper proposes a load dispatch model for energy management system (EMS) in a DC microgrid comprising solar (PV), wind power, diesel generator, and battery energy storage system. In the grid connected mode of operation, it facilitates a two way transaction of power between the microgrid and utility. The EMS with proposed model gave significant cost savings for the microgrid owner. In particular, application of the genetic algorithm based method resulted in optimal operation and maintenance costs as against the pattern search algorithm based method.