Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Characterization of Nonchemotactic CheZ Mutants of Escherichia coli

ABSTRACT The Escherichia coli CheZ protein stimulates dephosphorylation of CheY, a response regulator in the chemotaxis signal transduction pathway, by an unknown mechanism. Genetic analysis of CheZ has lagged behind biochemical and biophysical characterization. To identify putative regions of functional importance in CheZ, we subjected cheZ to random mutagenesis and isolated 107 nonchemotactic CheZ mutants. Missense mutations clustered in six regions of cheZ, whereas nonsense and frameshift mutations were scattered reasonably uniformly across the gene. Intragenic complementation experiments showed restoration of swarming activity when compatible plasmids containing genes for the truncated CheZ1–189 peptide and either CheZA65V, CheZL90S, or CheZD143G were both present, implying the existence of at least two independent functional domains in each chain of the CheZ dimer. Six mutant CheZ proteins, one from each cluster of loss-of-function missense mutations, were purified and characterized biochemically. All of the tested mutant proteins were defective in their ability to dephosphorylate CheY-P, with activities ranging from 0.45 to 16% of that of wild-type CheZ. There was good correlation between the phosphatase activity of CheZ and the ability to form large chemically cross-linked complexes with CheY in the presence of the CheY phosphodonor acetyl phosphate. In consideration of both the genetic and biochemical data, the most severe functional impairments in this set of CheZ mutants seemed to be concentrated in regions which are located in a proposed large N-terminal domain of the CheZ protein.
Serum uric acid, diuretic treatment and risk of cardiovascular events in the Systolic Hypertension in the Elderly Program (SHEP)

Objective To assess longitudinally the association of serum uric acid and its change due to diuretic treatment with cardiovascular events in hypertensive patients. Design Cohort study in a randomized trial. Setting Cohort of hypertensive patients. Participants A total of 4327 men and women, aged ≥ 60 years, with isolated systolic hypertension, randomized to placebo or chlorthalidone, with the addition of atenolol or reserpine if needed, were observed for 5 years. Main outcome measures Major cardiovascular events, coronary events, stroke and all-cause mortality. Results Cardiovascular event rates for quartiles of baseline serum uric acid were: I, 32.7 per 1000 person-years; II, 34.5 per 1000 person-years; III, 38.1 per 1000 person-years; and IV, 41.4 per 1000 person-years (P for trend = 0.02). The adjusted hazard ratio (HR), of cardiovascular events for the highest quartile of serum uric acid versus the lowest quartile was 1.32 (95% CI, 1.03–1.69). The benefit of active treatment was not affected by baseline serum uric acid. After randomization, an increase of serum uric acid < 0.06 mmol/l (median change) in the active treatment group was associated with a HR of 0.58 (0.37–0.92) for coronary events compared with those with a serum uric acid increase ≥ 0.06 mmol/l. This difference was not explained by blood pressure effects. Those with a serum uric acid increase ≥ 0.06 mmol/l in the active treatment group had a similar risk of coronary events as the placebo group. Conclusions Serum uric acid independently predicts cardiovascular events in older persons with isolated systolic hypertension. Monitoring serum uric acid change during diuretic treatment may help to identify patients who will most benefit from treatment.
Nitrogen Uptake by Perennial and Invasive Annual Grass Seedlings: Nitrogen Form Effects

Mention of trade names or commercial products is solely for the purpose of providing speciﬁ c information and does not imply recommendation or endorsement by the USDA-ARS. Research was funded in part by USDA Grant no. 97-38300-4892. Soil Sci. Soc. Am. J. 73:1864-1870doi:10.2136/sssaj2008.0334Received 16 Oct. 2008. *Corresponding author (Charles.MacKown@mac.com). © Soil Science Society of America677 S. Segoe Rd. Madison WI 53711 USAAll rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.
Improving kernel Fisher discriminant analysis for face recognition

This work is a continuation and extension of our previous research where kernel Fisher discriminant analysis (KFDA), a combination of the kernel trick with Fisher linear discriminant analysis (FLDA), was introduced to represent facial features for face recognition. This work makes three main contributions to further improving the performance of KFDA. First, a new kernel function, called the cosine kernel, is proposed to increase the discriminating capability of the original polynomial kernel function. Second, a geometry-based feature vector selection scheme is adopted to reduce the computational complexity of KFDA. Third, a variant of the nearest feature line classifier is employed to enhance the recognition performance further as it can produce virtual samples to make up for the shortage of training samples. Experiments have been carried out on a mixed database with 125 persons and 970 images and they demonstrate the effectiveness of the improvements.
The fungal pathogen Cochliobolus heterostrophus responds to maize phenolics: novel small molecule signals in a plant‐fungal interaction

The transcription factor ChAP1 of the fungal pathogen of maize, Cochliobolus heterostrophus, responds to oxidative stress by migration to the nucleus and activation of antioxidant genes. Phenolic and related compounds found naturally in the host also trigger nuclear localization of ChAP1, but only slight upregulation of some antioxidant genes. ChAP1 thus senses phenolic compounds without triggering a strong antioxidant response. We therefore searched for genes whose expression is regulated by phenolic compounds and/or ChAP1. The C. heterostrophus genome contains a cluster of genes for metabolism of phenolics. One such gene, catechol dioxygenase CCHD1, was induced at least 10‐fold by caffeic and coumaric acids. At high phenolic concentrations (≥ 1.6 mM), ChAP1 is needed for maximum CCHD1 expression. At micromolar levels of phenolics CCHD1 is as strongly induced in chap1 mutants as in the wild type. The pathogen thus detects phenolics by at least two signalling pathways: one causing nuclear retention of ChAP1, and another triggering induction of CCHD1 expression. The low concentrations required for induction of CCHD1 indicate fungal receptors for plant phenolics. Symbiotic and pathogenic bacteria are known to detect phenolics, and our findings generalize this to a eukaryotic pathogen. Phenolics and related compounds thus provide a ubiquitous plant‐derived signal.
Outer Pore Residues Control the H+ and K+ Sensitivity of the Arabidopsis Potassium Channel AKT3 Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.003244.

The Arabidopsis phloem channel AKT3 is the founder of a subfamily of shaker-like plant potassium channels characterized by weak rectification, Ca2+ block, proton inhibition, and, as shown in this study, K+ sensitivity. In contrast to inward-rectifying, acid-activated K+ channels of the KAT1 family, extracellular acidification decreases AKT3 currents at the macroscopic and single-channel levels. Here, we show that two distinct sites within the outer mouth of the K+-conducting pore provide the molecular basis for the pH sensitivity of this phloem channel. After generation of mutant channels and functional expression in Xenopus oocytes, we identified the His residue His-228, which is proximal to the K+ selectivity filter (GYGD) and the distal Ser residue Ser-271, to be involved in proton susceptibility. Mutations of these sites, H228D and S271E, drastically reduced the H+ and K+ sensitivity of AKT3. Although in K+-free bath solutions outward K+ currents were abolished completely in wild-type AKT3, S271E as well as the AKT3-HDSE double mutant still mediated K+ efflux. We conclude that the pH- and K+-dependent properties of the AKT3 channel involve residues in the outer mouth of the pore. Both properties, H+ and K+ sensitivity, allow the fine-tuning of the phloem channel and thus seem to represent important elements in the control of membrane potential and sugar loading.
Surgical Strategy for Hilar Cholangiocarcinoma of the Left-Side Predominance: Current Role of Left Trisectionectomy

Objective:To evaluate recent surgical strategy for hilar cholangiocarcinoma (HC) of the left-side predominance. Background:When employing left hemihepatectomy (LH) for HC, vasculobiliary anatomy of the right liver often makes it difficult to achieve a tumor-free margin of the right posterior sectional bile duct (RPSBD). Because left trisectionectomy (LTS) can produce a longer resection margin for the RPSBD, we have expanded the indications for LTS over the last 5 years. Methods:Sixty-one consecutive patients underwent left-sided hepatectomy for HC, divided into 2 groups according to the operative periods: period 1 (2001–2007; n = 29) and period 2 (2008–2012; n = 32). Clinicopathological outcomes of the groups were compared. The difference in the length of the resectable RPSBD between LH and LTS was radiologically investigated using multidetector-row computed tomography. Results:The proportion of LTS increased from 10.3% (3/29) in period 1 to 46.9% (15/32) in period 2. R0 resection rates were also improved in period 2. The most common margin positive site in period 1 was the stump of the proximal bile duct; high rates of positive RPSBD stump were noted after LH. The positive proximal ductal margin ratio decreased significantly in period 2. The difference in the length of resectable RPSBD between LH and LTS was 9.0 ± 1.3 mm. There was no mortality in period 2, even after LTS. Conclusions:LTS for HC of the left-side predominance improved R0 resection rates without affecting postoperative mortality. LTS should be aggressively performed in patients with appropriate hepatic function, even if tumors are possibly resectable by LH.
Print and publishing and the future of Augmented Reality

For Augmented Reality to reach beyond novelty (the simple “wow” factor) and become utilitarian and enjoyable regardless of where the user works or plays, there will need to be: • a nearly infinite amount of content, just as there is today on other digital platforms (e.g., the Web), • an easy system for the owners of content to build or find complementary digital data and have their content be viewed and associated with additional digital information in AR-assisted applications, and • many options for end users to reach the content and experience the AR enhancements.
Barriers to Improving Diabetes Care for Blacks

In the spring of 1989, the University of Michigan Diabetes Research and Training Center (MDRTC) convened a Task Force on Diabetes and the Black Population. This editorial is based on that task force report, which was issued on 15 January 1990. The mission of the task force was to identify potential barriers to the translation of scientific knowledge into improved health care and health for blacks with diabetes. Although it is known that diabetes affects a disproportionate number of black Americans, there is a paucity of information about the causes and effects of this burden. We hope this editorial contributes to a dialogue within the diabetes community that will lead to an increasingly articulated and tangible commitment to reducing the disproportionate burden that diabetes places on African Americans and other minorities in the United States. (94/10,000), and 108% higher than for white men (88/10,000; 1). In 1987, the age-adjusted rate of hospital discharges for diabetic ketoacidosis among black men with diabetes was 24.7/1000. This was nearly threefold higher than the corresponding rate of 8.7/ 1000 white men with diabetes (1). Similar discrepancies exist between black and white women with diabetes. When end-stage renal disease incidence is calculated with diabetic population denominators, the rates for black men and women are more than twice those for white men and women (1). Finally, the hospital discharge rates for lower-extremity amputation are consistently higher for blacks with diabetes than for whites with diabetes. The relative risks among blacks is —1.5to 2-fold higher compared with whites (1). These data confirm that African Americans are at increased risk for both diabetes and its complications. Many of the complications of diabetes are preventable through behavioral changes and preventative health-care services (2).
Salpingostomy in the treatment of hydrosalpinx: a systematic review and meta-analysis.

STUDY QUESTION What is the chance of natural conception when salpingostomy is used to treat hydrosalpinx? SUMMARY ANSWER The natural clinical pregnancy rate following salpingostomy is 27%, in the hands of experienced surgeons who publish their results. WHAT IS KNOWN ALREADY Tubal surgery is not commonly offered for women with hydrosalpinges since the advent of assisted conception treatment. This is the first systematic review to investigate natural conception rates following salpingostomy in the treatment of hydrosalpinx. STUDY DESIGN, SIZE, DURATION A systematic review and meta-analysis of 22 observational studies encompasses 2810 patients undergoing salpingostomy and attempting natural conception. PARTICIPANTS/MATERIALS, SETTING, METHODS Literature searches were conducted to retrieve observational studies which reported salpingostomy for hydrosalpinx. Databases searched included MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials and CINAHL, with no language restriction. Only studies that focused on salpingostomy (rather than other tubal conserving surgeries) for the treatment of hydrosalpinx were included. A total of 22 studies matched the inclusion criteria. MAIN RESULTS AND THE ROLE OF CHANCE The pooled natural clinical pregnancy rate from the 22 observational studies (including 2810 patients) was 27% (95% confidence interval (CI): 25-29%) after salpingostomy was performed for hydrosalpinx. The cumulative clinical pregnancy rates were 8.7% (95% CI: 6.6-11.5%) at 6 months, 13.3% (95% CI: 10.6-16.7%) at 9 months, 20.0% (95% CI: 17.5-22.8%) at 12 months, 21.2% (95% CI: 18.6-24.1%) at 18 months and 25.5% (95% CI: 22.2-29.4%) at 24 months after salpingostomy. The pooled live birth rate (10 studies, 1469 patients) was 25% (95% CI: 22-28%) after salpingostomy was performed for hydrosalpinx. The pooled ectopic pregnancy rate (19 studies, 2662 patients) was 10% (95% CI: 9-11%). The pooled miscarriage rate (seven studies, 924 patients) was 7% (95% CI: 6-9%). The included studies scored well on the Newcastle Ottawa quality assessment scale. LIMITATIONS, REASONS FOR CAUTION Strict inclusion criteria were used in the conduct of the systematic review. However, the studies included are clinically heterogeneous in many aspects including patient characteristics, surgical technique and duration of follow-up after salpingostomy. WIDER IMPLICATIONS OF THE FINDINGS The findings of this systematic review suggest that salpingostomy is an alternative treatment strategy to tubal clipping or salpingectomy in patients presenting to fertility services with hydrosalpinx. Further prospective, large and high quality studies are needed to identify the subpopulation that would most benefit from tube conserving surgery. STUDY FUNDING/COMPETING INTERESTS No external funding was either sought or obtained for this study. The authors have no competing interests to declare. TRIAL REGISTRATION NUMBER N/A.
Conductive inkjet printed ultra-wideband (UWB) planar monopole antenna on low cost flexible PET substrate material

Printed antennas on flexible substrate material are highly desirable for flexible circuits and wearable applications. An ultra-wideband (UWB) printed planar monopole antenna operating at 3.4-12 GHz was designed, modeled, fabricated, and tested for scattering parameters and radiation pattern response. The measured reflection coefficient magnitude for the fabricated antenna exhibits a bandwidth of 8.6 GHz, with near omnidirectional radiation patterns. For the sake of brevity, only some selected results are presented here.
On the Capacitated Controller Placement Problem in Software Defined Networks

Controller placement is a key problem in software defined networks (SDNs). Previously, the solution to this problem only focused on propagation latency but ignored the load of controllers, which is a critical factor in real networks. In this letter, we define a capacitated controller placement problem (CCPP), taking into consideration the load of controllers, and introduce an efficient algorithm to solve the problem. The evaluation shows that the new strategy can significantly reduce the number of required controllers, reduce the load of the maximum-load controller, and reduce the radius stretches compared with the K-center strategy with dynamic controller provision or dynamic scheduling.
Control of plasmid DNA replication by iterons: no longer paradoxical

Replication origins of a family of bacterial plasmids have multiple sites, called iterons, for binding a plasmid‐specific replication initiator protein. The iteron–initiator interactions are essential for plasmid replication as well as for inhibition of plasmid over‐replication. The inhibition increases with plasmid copy number and eventually shuts plasmid replication off completely. The mechanism of inhibition appears to be handcuffing, the coupling of origins via iteron‐bound initiators that block origin function. The probability of a trans‐reaction such as handcuffing is expected to increase with plasmid copy number and diminish with increases in cell volume, explaining how the copy number can be maintained in a growing cell. Control is also exerted at the level of initiator synthesis and activation by chaperones. We propose that increases in active initiators promote initiation by overcoming handcuffing, but handcuffing dominates when the copy number reaches a threshold. Handcuffing should be ultrasensitive to copy number, as the negative control by iterons can be stringent (switch‐like).
Simple Method for Screening Candida Species Isolates for the Presence of Secreted Proteinases: a Tool for the Prediction of Successful Inhibitory Treatment

ABSTRACT The yeasts of the genus Candida are opportunistic pathogens associated with the rising incidence of life-threatening infections in immunocompromised individuals. Secretion of aspartic proteinases has been determined to be one of the virulence factors of the pathogenic Candida species. To analyze the extracellular proteolytic activities of a large number of Candida clinical isolates, we developed a screening system based on a solid medium containing hemoglobin as the sole nitrogen source. The cleavage of hemoglobin by the secreted proteinases results in formation of clearance zones. The visibility of such zones was enhanced by addition of an acid-base indicator. Using this system, we assessed 245 clinical isolates of Candida from patients in the hospital of the Faculty of Medicine, Palacky University, Olomouc, Czech Republic, for the presence of secreted aspartic proteases (Saps). We also used the test plates for rapid semiquantitative testing of Sap inhibitors. Most of the pepstatin analogs affected the formation of the zones of clearance as well as the growth of Candida albicans, C. tropicalis, and C. parapsilosis colonies. By contrast, the human immunodeficiency virus proteinase inhibitors saquinavir, ritonavir, nelfinavir, and indinavir had no effect on the Candida strains tested. These results are in agreement with the inhibition constants obtained for the individual inhibitors with purified Saps. Thus, the plates containing hemoglobin proved to be an appropriate tool for the rapid and reliable assessment of Sap production and inhibition.
Follicular low‐grade non‐Hodgkin's lymphoma: Long‐term outcome with or without tumor progression

Long‐term outcome for 127 patients with follicular low‐grade lymphoma was investigated. Therapy included radiotherapy (n = 23), low toxicity chemotherapy with or without radiotherapy (n = 76), or more intensive chemotherapy (n = 22). 6 patients had no initial therapy. Complete remission was obtained in 67% of patients. For patients under 60 years of age median survival was 8.7 yr compared with 3.8 yr for older patients, but survival from lymphoma was identical for the two age‐groups: 75% at 5 yr, and 58% at 10 yr. The relatively low tumor mortality contrasted with a relapse‐free survival of 30% at 10 yr, and relapse 8–9 yr after first remission. Examining the disease topography and the stability of histologic subtype in 78 patients with recurrent lymphoma, two types of relapse with different prognoses were identified: 1) with tumor progression (lymphoma dissemination to atypical extranodal sites and/or histologic conversion to an intermediate/high‐grade lymphoma) seen in 56% of patients with a survival from lymphoma of 13% at 10 yr; and 2) without tumor progression (involvement of nodal sites, and unchanged histology) seen in 44% with a survival from lymphoma of 77% at 10 yr. Actuarial risk of tumor progression was 44% at 5 yr, and 67% at 10 yr. Except from the negative impact of a large tumor burden, it was not possible to identify patients with high risk for tumor progression. More important than all pretreatment factors was poor response to initial therapy (p = 0.0001). Due to lack of reliable risk factors, it is recommended that all younger patients be treated with the intention of achieving complete remission; a significant fraction might be curable.
A fundamental limit on delay estimation using partially correlated speckle signals

Delay estimation is used in ultrasonic imaging to estimate blood or soft tissue motion, to measure echo arrival time differences for phase aberration correction, and to estimate displacement for tissue elasticity measurements. In each of these applications delay estimation is performed using speckle signals which are at least partially decorrelated relative to one another. Delay estimates which utilize such data are subject to large errors known as false peaks and smaller magnitude errors known as jitter. While false peaks can sometimes be removed through nonlinear processing, jitter errors place a fundamental limit on the performance of delay estimation techniques. The authors apply the Cramer-Rao Lower Bound to derive an analytical expression which predicts the magnitude of jitter errors incurred when estimating delays using radio frequency (RF) data from speckle targets. The analytical expression presented includes the effects of signal decorrelation due to physical processes, corruption by electronic noise, and a number of other factors. Simulation results are presented which show that the performance of the normalized cross correlation algorithm closely matches theoretical predictions. These results indicate that for poor signal to noise ratios (0 dB) a small improvement in signal to noise ratio can dramatically reduce jitter magnitude. At high signal to noise ratios (30 dB) small amounts of signal decorrelation can significantly increase the magnitude of jitter errors. <<ETX>>