Miracle-dz/UniFAR-FTUs huggingface dataset:
Impairments due to the interplay between node crosstalk and nonlinear propagation in all optical transport networks

All optical transport networks should be designed to avoid the detrimental effect due to in-band crosstalk that may arise from nonideal components in optical nodes. In this letter, we numerically investigate the nonlinear propagation of signal with in-band crosstalk, finding much greater penalties than were previously established in the linear regime. This effect is observed in the anomalous dispersion regime, and the highest impact is obtained for a nonzero frequency detuning between the optical carriers of the signal and of the crosstalk. The phenomenon, which can be explained in terms of the modulation instability, can result in reduced tolerance to crosstalk.
Ferritin and ferritin isoforms II: Protection against uncontrolled cellular proliferation, oxidative damage and inflammatory processes

Abstract Ferritin is a major iron storage protein involved in the regulation of iron availability. Each ferritin molecule comprises 24 subunits. Various combinations of H-subunits and L-subunits make up the 24-subunit protein structure and these ferritin isoforms differ in their H-subunit to L-subunit ratio, as well as in their metabolic properties. Ferritin is an acute-phase protein and its expression is up-regulated in conditions such as uncontrolled cellular proliferation, in any condition marked by excessive production of toxic oxygen radicals, and by infectious and inflammatory processes. Under such conditions ferritin up-regulation is predominantly stimulated by increased reactive oxygen radical production and by cytokines. The major function of ferritin in these conditions is to reduce the bio-availability of iron in order to stem uncontrolled cellular proliferation and excessive production of reactive oxygen radicals. Ferritin is not, however, indiscriminately up-regulated in these conditions as a marked shift towards a predominance in H-subunit rich ferritins occurs. Preliminary indications are that, while the L-subunit primarily fulfils the conventional iron storage role, the H-subunit functions primarily as rapid regulator of iron availability, and perhaps indirectly as regulator of other cellular processes. It is suggested that the optimum differential expression of the two subunits differ for different cells and under different conditions and that the expression of appropriate isoferritins offers protection against uncontrolled cellular proliferation, oxidative stress and against side effects of infectious and inflammatory conditions.
Adaptive Optimal Control of Unknown Constrained-Input Systems Using Policy Iteration and Neural Networks

This paper presents an online policy iteration (PI) algorithm to learn the continuous-time optimal control solution for unknown constrained-input systems. The proposed PI algorithm is implemented on an actor-critic structure where two neural networks (NNs) are tuned online and simultaneously to generate the optimal bounded control policy. The requirement of complete knowledge of the system dynamics is obviated by employing a novel NN identifier in conjunction with the actor and critic NNs. It is shown how the identifier weights estimation error affects the convergence of the critic NN. A novel learning rule is developed to guarantee that the identifier weights converge to small neighborhoods of their ideal values exponentially fast. To provide an easy-to-check persistence of excitation condition, the experience replay technique is used. That is, recorded past experiences are used simultaneously with current data for the adaptation of the identifier weights. Stability of the whole system consisting of the actor, critic, system state, and system identifier is guaranteed while all three networks undergo adaptation. Convergence to a near-optimal control law is also shown. The effectiveness of the proposed method is illustrated with a simulation example.
Chromosomal mapping of mutations affecting glycerol and glucose catabolism in Pseudomonas aeruginosa PAO

Mutations causing deficiencies in the inducible, membrane-associated sn-glycerol-3-phosphate dehydrogenase (glpD) and in inducible glucose transport (glcT) were mapped on the Pseudomonas aeruginosa PAO1 chromosome by using the generalized transducing phages F116L and G101. These mutations, in separate catabolic regulatory units, were cotransducible with a previously described cluster of carbohydrate catabolic gene loci (zwf-1 eda-9001 edd-1) that maps at ca. 50 to 53 min on the chromosome. Mutant strain PFB362 (glcT1) did not transport glucose and did not produce a functional, periplasmic, glucose-binding protein that is required for glucose transport. This mutation was cotransducible with zwf-1 (70%), nalA (29%), and phe-2 (19%) but not with glpD1 or leu-10. The glpD1 mutation in strain PRP408 was cotransducible with zwf-1 (5%), eda-9001 (4%), and edd-1 (1%) and also with ami-151 (17%) and phe-2 (33%). These results expand the number of known carbohydrate catabolism genes that are clustered in the 50- to 55-min region of the PAO1 chromosome and allow us to propose the following relative gene order: ami-151 glpD1 phe-2 nalA zwf-1 eda-9001 edd-1 glcT1 leu-10. Three independently obtained nal determinants for high-level resistance to nalidixic acid, which were employed in these studies, exhibited similar cotransduction frequencies with several flanking marker mutations.
Cyclic AMP Regulates Bacterial Persistence through Repression of the Oxidative Stress Response and SOS-Dependent DNA Repair in Uropathogenic Escherichia coli

ABSTRACT Bacterial persistence is a transient, nonheritable physiological state that provides tolerance to bactericidal antibiotics. The stringent response, toxin-antitoxin modules, and stochastic processes, among other mechanisms, play roles in this phenomenon. How persistence is regulated is relatively ill defined. Here we show that cyclic AMP, a global regulator of carbon catabolism and other core processes, is a negative regulator of bacterial persistence in uropathogenic Escherichia coli, as measured by survival after exposure to a β-lactam antibiotic. This phenotype is regulated by a set of genes leading to an oxidative stress response and SOS-dependent DNA repair. Thus, persister cells tolerant to cell wall-acting antibiotics must cope with oxidative stress and DNA damage and these processes are regulated by cyclic AMP in uropathogenic E. coli. IMPORTANCE Bacterial persister cells are important in relapsing infections in patients treated with antibiotics and also in the emergence of antibiotic resistance. Our results show that in uropathogenic E. coli, the second messenger cyclic AMP negatively regulates persister cell formation, since in its absence much more persister cells form that are tolerant to β-lactams antibiotics. We reveal the mechanism to be decreased levels of reactive oxygen species, specifically hydroxyl radicals, and SOS-dependent DNA repair. Our findings suggest that the oxidative stress response and DNA repair are relevant pathways to target in the design of persister-specific antibiotic compounds. IMPORTANCE Bacterial persister cells are important in relapsing infections in patients treated with antibiotics and also in the emergence of antibiotic resistance. Our results show that in uropathogenic E. coli, the second messenger cyclic AMP negatively regulates persister cell formation, since in its absence much more persister cells form that are tolerant to β-lactams antibiotics. We reveal the mechanism to be decreased levels of reactive oxygen species, specifically hydroxyl radicals, and SOS-dependent DNA repair. Our findings suggest that the oxidative stress response and DNA repair are relevant pathways to target in the design of persister-specific antibiotic compounds.
Induced label graphoidal graphs

Abstract Let G be a non-trivial, simple, finite, connected and undirected graph of order n and size m. An induced acyclic graphoidal decomposition (IAGD) of G is a collection ψ of non-trivial and internally disjoint induced paths in G such that each edge of G lies in exactly one path of ψ. For a labeling f : V → {1, 2, 3, . ,n}, let ↑ Gf be the directed graph obtained by orienting the edges uv of G from u to v, provided f(u) < f(v). If the set ψf of all maximal directed induced paths in ↑ Gf with directions ignored is an induced path decomposition of G, then f is called an induced graphoidal labeling of G and G is called an induced label graphoidal graph. The number ηil = min{|ψf| : f is an induced graphoidal labeling of G} is called the induced label graphoidal decomposition number of G. In this paper we introduce and study the concept of induced graphoidal labeling as an extension of graphoidal labeling.
The actin-binding protein profilin is required for germline stem cell maintenance and germ cell enclosure by somatic cyst cells

Specialized microenvironments, or niches, provide signaling cues that regulate stem cell behavior. In the Drosophila testis, the JAK-STAT signaling pathway regulates germline stem cell (GSC) attachment to the apical hub and somatic cyst stem cell (CySC) identity. Here, we demonstrate that chickadee, the Drosophila gene that encodes profilin, is required cell autonomously to maintain GSCs, possibly facilitating localization or maintenance of E-cadherin to the GSC-hub cell interface. Germline specific overexpression of Adenomatous Polyposis Coli 2 (APC2) rescued GSC loss in chic hypomorphs, suggesting an additive role of APC2 and F-actin in maintaining the adherens junctions that anchor GSCs to the niche. In addition, loss of chic function in the soma resulted in failure of somatic cyst cells to maintain germ cell enclosure and overproliferation of transit-amplifying spermatogonia.
Engineering succinct DOM

We describe the engineering of Succinct DOM (SDOM), a DOM implementation, written in C++, which is suitable for in-memory representation of large static XML documents. SDOM avoids the use of pointers, and is based upon succinct data structures, which use an information-theoretically minimum amount of space to represent an object. SDOM gives a space-efficient in-memory representation, with stable and predictable memory usage. The space used by SDOM is an order of magnitude less than that used by a standard C++ DOM representation such as Xerces, but SDOM is extremely fast: navigation is in some cases faster than for a pointer-based representation such as Xerces (even for moderate-sized documents which can comfortably be loaded into main memory by Xerces). A variant, SDOM-CT, applies bzip-based compression to textual and attribute data, and its space usage is comparable with "queryable" XML compressors. Some of these compressors support navigation and/or querying (e.g. subpath queries) of the compressed file. SDOM-CT does not support querying directly, but remains extremely fast: it is several orders of magnitude faster for navigation than queryable XML compressors that support navigation (and only a few times slower than say Xerces).
Automated measurement of latent morphological features in the human corpus callosum

Our objective was to develop a novel factor‐based analysis of the morphology of the corpus callosum and assess its applicability to the study of normal development, intelligence, and other subject characteristics. The contour of the corpus callosum was defined in the midsagittal planes of the MRI scans of 325 subjects, 6 to 88 years of age. The contours were coregistered, rescaled, and resampled to 50 points that were then entered into a principal components analysis with varimax rotation. The analysis yielded 8 factors for the contours of 138 healthy subjects. A second analysis of contours from 187 subjects in a patient group extracted 8 similar factors. Correlations of factor scores with conventional measures of callosum shape supported the construct validity of the assignment of morphological features to each of the factors. Correlations of factor scores with age, sex, handedness, ventricular volume, and IQ demonstrated the predictive validity of the factor structure and helped to define the neural correlates of these subject characteristics. We conclude that factor‐based measures capture latent morphological features of the corpus callosum that are reliable and valid. Future studies will determine whether these novel measures are more closely related to neurobiologically important features of the corpus than are conventional measures of callosum size and shape. Hum. Brain Mapping 12:232–245, 2001. © 2001 Wiley‐Liss, Inc.
Category-specific difficulty naming with verbs in Alzheimer's disease

We studied 20 patients with Alzheimer's disease (AD) on a picture-naming task consisting of frequency-matched pairs of nouns and verbs that were homophonic and homographic (e.g., paint). Intragroup comparisons revealed that verb naming is significantly more difficult for patients with AD than noun naming. An error analysis demonstrated that patients with AD produce significantly more semantic and descriptive errors for verbs than nouns. We correlated verb naming and noun naming with measures of grammatical comprehension, lexical retrieval, and visuoperceptual processing, but there were no selective effects for verbs compared with nouns. Differences in the mental representation of concepts underlying verbs and nouns may account, in part, for the relative difficulty naming with verbs in AD. NEUROLOGY 1996;47: 178-182
Turbofan Jet Noise Reduction via Deflection of the Bypass Stream

We describe a parametric experimental study of noise reduction via de ection of the secondary stream in dual-stream jets. The jets simulated the exhaust of turbofan engines with bypass ratios 4.5 and 6.0. The secondary (bypass) stream was de ected downward by means of vanes installed inside the bypass duct. Variables included the number of vanes, vane angle of attack, azimuthal placement, and axial position. The shape of the bypass duct was also varied. Noise measurements were converted to estimates of yover and sideline e ective perceived noise level (EPNL). The quietest con gurations used a rapidly convergent bypass duct with vanes installed in the proximity of the duct exit. Two pairs of vanes, installed at azimuth angles 70 and 110 deg with respect to the vertical, constitutes one of the most promising con gurations. Substantial bene t in EPNL occurs when the vanes have dissimilar angles of attack, with the upper pair at smaller incidence than the lower pair. The best arrangement o ered a 5.3-dB reduction in the sum of yover and sideline EPNL.
Meta-analysis: the effects of smoking on the disposition of two commonly used antipsychotic agents, olanzapine and clozapine

Objective To clarify the effects of smoking on the disposition of two commonly used antipsychotics, olanzapine and clozapine, and to create standards to adjust the doses of these drugs in clinical practice based on the smoking status. Design A meta-analysis was conducted by searching MEDLINE, Scopus and the Cochrane Library for relevant prospective and retrospective studies. Included studies We included the studies that investigated the effects of smoking on the concentration to dose (C/D) ratio of olanzapine or clozapine. Primary outcome measure The weighted mean difference was calculated using a DerSimonian-Laird random effects model, along with 95% CI. Results Seven association studies, comprising 1094 patients (652 smokers and 442 non-smokers) with schizophrenia or other psychiatric disorders, were included in the meta-analysis of olanzapine. The C/D ratio was significantly lower in smokers than in non-smokers (p<0.00001), and the mean difference was −0.75 (ng/mL)/(mg/day) (95% CI −0.89 to −0.61). Therefore, it was estimated that if 10 and 20 mg/day of olanzapine would be administered to smokers, about 7 and 14 mg/day, respectively, should be administered to non-smokers in order to obtain the equivalent olanzapine concentration. Four association studies of clozapine were included in the meta-analysis of clozapine, comprising 196 patients (120 smokers and 76 non-smokers) with schizophrenia or other psychiatric disorders. The C/D ratio was significantly lower in smokers than in non-smokers (p<0.00001), and the mean difference was −1.11 (ng/mL)/(mg/day) (95% CI −1.53 to −0.70). Therefore, it was estimated that if 200 and 400 mg/day of clozapine would be administered to smokers, about 100 and 200 mg/day, respectively, should be administered to non-smokers. Conclusions We suggest that the doses of olanzapine and clozapine should be reduced by 30% and 50%, respectively, in non-smokers compared with smokers in order to obtain an equivalent olanzapine or clozapine concentration.
High Uric Acid Ameliorates Indoxyl Sulfate-Induced Endothelial Dysfunction and Is Associated with Lower Mortality among Hemodialysis Patients

High uric acid (UA) can act as a pro-oxidant in normal physiological conditions; however, emerging evidence is still debatable with regard to the association between high UA and poor outcomes among chronic hemodialysis (HD) patients. In the present study, 27,229 stable prevalent HD patients were enrolled and divided into four groups according to the quartiles of baseline UA concentration, and 5737 died during a median follow-up of 38 months. Multivariate Cox regression analysis showed that a UA level of <6.1 mg/dL was associated with a higher risk of all-cause mortality compared with a UA level of >8.1 mg/dL [HR, 1.20, 95% CI (1.10–1.31)] adjusting for baseline demographic and biochemical parameters. Moreover, a UA level of <6.1 mg/dL was associated with greater risks of cardiovascular mortality [HR, 1.26, 95% CI (1.13–1.41)] and stroke-related mortality [HR, 1.59, 95% CI (1.12–2.25)], respectively. In vitro experiments further showed an increase in oxidative stress and an inhibition nitric oxide synthesis by indoxyl sulfate (IS) in human aortic endothelial cells, which were significantly attenuated by UA in a dose-dependent manner. We concluded that higher UA in serum was associated with lower risk of all-cause and cardiovascular mortality among HD patients probably through its antioxidant property in ameliorating the IS-related vascular toxicity.
Experiences and Future Challenges of Bioleaching Research in South Korea

This article addresses the state of the art of bioleaching research published in South Korean Journals. Our research team reviewed the available articles registered in the Korean Citation Index (KCI, Korean Journal Database) addressing the relevant aspects of bioleaching. We systematically categorized the target metal sources as follows: mine tailings, electronic waste, mineral ores and metal concentrates, spent catalysts, contaminated soil, and other materials. Molecular studies were also addressed in this review. The classification provided in the present manuscript details information about microbial species, parameters of operation (e.g., temperature, particle size, pH, and process length), and target metals to compare recoveries among the bioleaching processes. The findings show an increasing interest in the technology from research institutes and mineral processing-related companies over the last decade. The current research trends demonstrate that investigations are mainly focused on determining the optimum parameters of operations for different techniques and minor applications at the industrial scale, which opens the opportunity for greater technological developments. An overview of bioleaching of each metal substrate and opportunities for future research development are also included.
Expert Review of Non-Hodgkin’s Lymphomas in a Population-Based Cancer Registry

Incidence rates of non-Hodgkin’s lymphomas (NHLs) have nearly doubled in recent decades. Understanding the reasons behind these trends will require detailed surveillance and epidemiological study of NHL subtypes in large populations, using cancer registry or other multicenter data. However, little is known regarding the reliability of NHL diagnosis and subtype classification in such data, despite implications for the accuracy of incidence statistics and studies. Expert pathological re-review was completed for 1526 NHL patients who were reported to the Greater Bay Area Cancer Registry and who participated in a large population-based case-control study. Agreement of registry diagnosis with expert diagnosis and with International Classification of Diseases for Oncology-2 (Working Formulation) subtype classifications was measured with positive predictive values and κ statistics. Agreement of registry and expert diagnoses was high (98%). Thirty patients were found on review not to have NHL; most of these had leukemia. For subtypes, agreement of registry and expert classification was more moderate (59%). Agreement varied substantially by subtype from 5% to 100% and was 77% for the most common subtype, diffuse large cell lymphoma. Seventy-seven percent of 128 registry-unclassified lymphomas were assigned a subtype on re-review. Our analyses suggest excellent diagnostic reliability but poorer subtype reliability of NHL in cancer registry data information that is critical to the interpretation of lymphoma time trends. Thus, overall NHL incidence and survival statistics from the early 1990s are probably accurate, but subtype-specific statistics could be substantially biased, especially because of high (15–20%) proportions of unclassified lymphomas.
p21 Functions to Maintain Quiescence of p27-deficient Hepatocytes*

Hepatocytes rarely proliferate in the healthy adult liver. We explored the roles of the cyclin kinase inhibitors p21 and p27 in maintaining hepatocyte quiescence. p27 is expressed throughout the wild-type liver, but the related protein p21 was not detected. However, p21 was detected in livers of p27-deficient mice. Increased p21 protein levels did not result from an increase in p21 mRNA expression, indicating that p21 expression is regulated post-transcriptionally. p21 protein levels increased in cultured primary hepatocytes treated with the proteasome inhibitor MG132 and cycloheximide, indicating that p21 expression is regulated at the level of protein stability in liver cells. Although increased expression of cyclin-dependent kinase (Cdk) 4, Cdk2, and proliferating cell nuclear antigen was detected in p27-deficient livers, increased hepatocyte proliferation was detected only in livers of mice deficient for both p21 and p27. In p27-deficient livers, p21 was found in complexes with Cdk2 and CdK4 and can compensate for the absence of p27. Our data indicate that cyclin kinase inhibitor activity is important for maintaining hepatocyte quiescence in the adult liver. Significant increases in p21 were detected in multiple tissues of mature p27-deficient mice compared with wild-type mice, suggesting that the ability of p21 to functionally substitute for p27 is not liver-specific.