Miracle-dz/UniFAR-FTUs huggingface dataset:
Copper Efflux Is Induced during Anaerobic Amino Acid Limitation in Escherichia coli To Protect Iron-Sulfur Cluster Enzymes and Biogenesis

ABSTRACT Adaptation to changing environments is essential to bacterial physiology. Here we report a unique role of the copper homeostasis system in adapting Escherichia coli to its host-relevant environment of anaerobiosis coupled with amino acid limitation. We found that expression of the copper/silver efflux pump CusCFBA was significantly upregulated during anaerobic amino acid limitation in E. coli without the supplement of exogenous copper. Inductively coupled plasma mass spectrometry analysis of the total intracellular copper content combined with transcriptional assay of the PcusC-lacZ reporter in the presence of specific Cu(I) chelators indicated that anaerobic amino acid limitation led to the accumulation of free Cu(I) in the periplasmic space of E. coli, resulting in Cu(I) toxicity. Cells lacking cusCFBA and another copper transporter, copA, under this condition displayed growth defects and reduced ATP production during fumarate respiration. Ectopic expression of the Fe-S cluster enzyme fumarate reductase (Frd), or supplementation with amino acids whose biosynthesis involves Fe-S cluster enzymes, rescued the poor growth of ΔcusC cells. Yet, Cu(I) treatment did not impair the Frd activity in vitro. Further studies revealed that the alternative Fe-S cluster biogenesis system Suf was induced during the anaerobic amino acid limitation, and ΔcusC enhanced this upregulation, indicating the impairment of the Fe-S cluster assembly machinery and the increased Fe-S cluster demands under this condition. Taken together, we conclude that the copper efflux system CusCFBA is induced during anaerobic amino acid limitation to protect Fe-S cluster enzymes and biogenesis from the endogenously originated Cu(I) toxicity, thus facilitating the physiological adaptation of E. coli.
Promoter Engineering for Enhanced P(3HB- co-4HB) Production by Halomonas bluephagenesis.

Promoters for the expression of heterologous genes in Halomonas bluephagenesis are quite limited, and many heterologous promoters function abnormally in this strain. Pporin, a promoter of the strongest expressed protein porin in H. bluephagenesis, is one of the few promoters available for heterologous expression in H. bluephagenesis, yet it has a fixed transcriptional activity that cannot be tuned. A stable promoter library with a wide range of activities is urgently needed. This study reports an approach to construct a promoter library based on the Pporin core region, namely, from the -35 box to the transcription start site, a spacer and an insulator. Saturation mutagenesis was conducted inside the promoter core region to significantly increase the diversity within the promoter library. The promoter library worked in both E. coli and H. bluephagenesis, covering a wide range of relative transcriptional strengths from 40 to 140 000. The library is therefore suitable for the transcription of many different heterologous genes, serving as a platform for protein expression and fine-tuned metabolic engineering of H. bluephagenesis TD01 and its derivative strains. H. bluephagenesis strains harboring the orfZ gene encoding 4HB-CoA transferase driven by selected promoters from the library were constructed, the best one produced over 100 g/L cell dry weight containing 80% poly(3-hydroxybutyrate- co-11 mol % 4-hydroxybutyrate) with a productivity of 1.59 g/L/h after 50 h growth under nonsterile fed-batch conditions. This strain was found the best for P(3HB- co-4HB) production in the laboratory scale.
Differences in Hydrogenase Gene Expression between Methanosarcina acetivorans and Methanosarcina barkeri

ABSTRACT Methanosarcina acetivorans C2A encodes three putative hydrogenases, including one cofactor F420-linked (frh) and two methanophenazine-linked (vht) enzymes. Comparison of the amino acid sequences of these putative hydrogenases to those of Methanosarcina barkeri and Methanosarcina mazei shows that each predicted subunit contains all the known residues essential for hydrogenase function. The DNA sequences upstream of the genes in M. acetivorans were aligned with those in other Methanosarcina species to identify conserved transcription and translation signals. The M. acetivorans vht promoter region is well conserved among the sequenced Methanosarcina species, while the second vht-type homolog (here called vhx) and frh promoters have only limited similarity. To experimentally determine whether these promoters are functional in vivo, we constructed and characterized both M. acetivorans and M. barkeri strains carrying reporter gene fusions to each of the M. acetivorans and M. barkeri hydrogenase promoters. Generally, the M. acetivorans gene fusions are not expressed in either organism, suggesting that cis-acting mutations inactivated the M. acetivorans promoters. The M. barkeri hydrogenase gene fusions, on the other hand, are expressed in both organisms, indicating that M. acetivorans possesses the machinery to express hydrogenases, although it does not express its own hydrogenases. These data are consistent with specific inactivation of the M. acetivorans hydrogenase promoters and highlight the importance of testing hypotheses generated by using genomic data.
Multi-column implementations for cache associativity

We propose two schemes for implementing higher associativity: the sequential multi-column cache, which is an extension of the column associative cache, and the parallel multi-column cache. In order to achieve the same access cycle time as that of a direct-mapped cache, data memory in the cache is organized into one bank in both schemes. We use the multiple MRU block technique to increase the first hit ratio, thus reducing the average access time. While the parallel multi-column cache performs the tag checking in parallel, the sequential multi-column cache sequentially searches through places in a set, and uses index information to filter out unnecessary probes. In the case of an associativity of 4, they both achieve the low miss rate of a 4-way set-associative cache. Our simulation results using ATUM traces show that both schemes can effectively reduce the average access time.
The Peptidoglycan of Mycobacterium abscessus Is Predominantly Cross-Linked by l,d-Transpeptidases

ABSTRACT Few therapeutic alternatives remain for the treatment of infections due to multiresistant Mycobacterium abscessus. Here we show that the peptidoglycans of the “rough” and “smooth” morphotypes contain predominantly 3→3 cross-links generated by l,d-transpeptidases, indicating that these enzymes are attractive targets for the development of efficient drugs.
Leading-one prediction scheme for latency improvement in single datapath floating-point adders

This paper describes the design of a Leading-one Predictor (LOP) for floating-point addition, with an exact determination of the shift amount required. Previous LOP proposals produce a shift amount which might be in error by one position, so that this error has to be corrected after the addition terminates, increasing the critical path. Our design incorporates a concurrent detection of this error so that the amount of shift is corrected before the actual shift, without increasing the latency. The scheme presented here is applicable to the common case of a single datapath floating-point addition in which the output of the adder is always positive. We estimate the reduction in the critical path and the increase in area.
Choroidal Thickness in Open-angle Glaucoma

Purpose:To examine choroidal thickness in open-angle glaucoma. Methods:The hospital-based case series study included a study group with patients with open-angle glaucoma and a control group. Choroidal thickness was measured by enhanced depth imaging by spectral domain optical coherence tomography. Results:The study group included 39 patients (71 eyes) and the control group consisted of 189 patients (228 eyes) with no significant difference between both groups in age (P=0.16) and refractive error (P=0.07). Choroidal thickness in the foveal region (P=0.18), at a distance of 1000 &mgr;m from the fovea (P=0.39), 2000 &mgr;m from the fovea (P=0.46), and 2500 &mgr;m from the fovea (P=0.53) did not vary significantly between both groups. In multivariable analysis with adjustment for age and refractive error, choroidal thickness at the fovea [P=0.12; regression coefficient B: minus−8.60; 95% confidence interval (CI): −19.3, 2.1], at a horizontal distance of 1000 &mgr;m from the fovea (P=0.30; regression coefficient B: −4.98; 95% CI: −14.3, 4.4), 2000 &mgr;m from the fovea (P=0.20; regression coefficient B: −20.9; 95% CI: −53.2, 11.3), and 2500 &mgr;m from the fovea (P=0.45; regression coefficient B: −2.70; 95% CI: −9.67, 4.27) was not significantly associated with the diagnosis of glaucoma. In binary regression analysis with adjustment for age and refractive error, presence of glaucoma was significantly associated neither with subfoveal choroidal thickness [P=0.12; odds ratio (OR): 0.997; 95% CI: 0.993, 1.001] nor with choroidal thickness at a horizontal distance of 1000 &mgr;m from the fovea (P=0.47; OR: 0.998; 95% CI: 0.993, 1.002), 2000 &mgr;m from the fovea (P=0.23; OR: 0.997; 95% CI: 0.993, 1.002), or 2500 &mgr;m from the fovea (P=0.46; OR: 0.998; 95% CI: 0.992, 1.004). Conclusions:After adjusting for age and refractive error, open-angle glaucoma was not significantly associated with a marked thinning or a thickening of the choroid in the foveal and parafoveal region.
A DSP with caches-a study of the GSM-EFR codec on the TI C6211

Texas Instruments has positioned the C6211 as the low cost member of its C62xx family of DSPs. The C6211 differs from the other devices in this family in that it has a new on-chip memory architecture that uses a two-level cache hierarchy, something not typically seen on a DSP. This paper presents results of a performance study of the TI C6211 running the GSM-EFR speech codec, an important benchmark application in digital cellular telephony. A detailed analysis of the cache performance shows that the caches, although small, are effective in maintaining good performance, even in a multi-programmed workload, where cache pollution affects the memory system performance.
System-on-a-chip bus architecture for embedded applications

Increasing levels of on-chip system integration means that more functional units need to be interconnected. To limit design effort and to allow for future reuse, this interconnection should be kept as simple and generic as possible. The need to limit clock cycle times and power consumption means that bus capacitance must be as low as possible. This can be done effectively by partitioning functional units onto discrete bus connections that are jointed by bus bridges. The paper describes the evolution of ARM system chip architectures of steadily increasing complexity and details a state-of-the-art design.
Symptoms and Signs of Thoracic Outlet Syndrome in Patients with Carpal Tunnel Syndrome

ABSTRACT Objective: To describe the prevalence and diagnostic value of positive symptoms and provocative signs of thoracic outlet syndrome [TOS] in patients with carpal tunnel syndrome [CTS]. Methods: A total of 93 symptomatic upper extremities in 56 consecutive patients referred for clinical and electrodiagnostic evaluation of suspected CTS were studied. Each patient was asked to describe their hand symptoms with overhead positioning [TOS symptom] and at nighttime [CTS symptom]. Physical examination included five provocative TOS signs [Roos, costoclavicular, Adson, Allen, and Halstead] and three provocative CTS signs [Tinel, Phalen, and carpal tunnel compression]. Results: A total of 60 out of 93 [65 percent] upper limbs had electrodiagnostic abnormalities compatible with CTS. Of them, 29 percent had symptom aggravation with overhead arm positioning, whereas 97 percent had nocturnal symptom aggravation. Nocturnal symptom aggravation was highly sensitive but not specific for CTS, whereas symptom aggravation with overhead positioning was specific but not sensitive. The likelihood of CTS was highest when there were both symptom aggravation at nighttime and overhead hand positioning [likelihood ratio = 4.1]. In total 55 percent of limbs with CTS had at least one positive provocative TOS sign compared to 76 percent of those without CTS. However, the presence of a positive TOS sign[s] was associated with the least likelihood of having CTS [likelihood ratio from 0.62 to 0.71]. Conclusions: Hand neurologic symptom aggravation when positioned overhead is specific for CTS and nocturnal symptom aggravation is sensitive. When both are present, CTS is 4.1 times as likely as when they are not present. Positive TOS provocative tests reduce the likelihood of CTS being present.
Structural Characterization of a Conserved, Calcium-Dependent Periplasmic Protease from Legionella pneumophila

ABSTRACT The bacterial dinucleotide second messenger c-di-GMP has emerged as a central molecule in regulating bacterial behavior, including motility and biofilm formation. Proteins for the synthesis and degradation of c-di-GMP and effectors for its signal transmission are widely used in the bacterial domain. Previous work established the GGDEF-EAL domain-containing receptor LapD as a central switch in Pseudomonas fluorescens cell adhesion. LapD senses c-di-GMP inside the cytosol and relays this signal to the outside by the differential recruitment of the periplasmic protease LapG. Here we identify the core components of an orthologous system in Legionella pneumophila. Despite only moderate sequence conservation at the protein level, key features concerning the regulation of LapG are retained. The output domain of the LapD-like receptor from L. pneumophila, CdgS9, binds the LapG ortholog involving a strictly conserved surface tryptophan residue. While the endogenous substrate for L. pneumophila LapG is unknown, the enzyme processed the corresponding P. fluorescens substrate, indicating a common catalytic mechanism and substrate recognition. Crystal structures of L. pneumophila LapG provide the first atomic models of bacterial proteases of the DUF920 family and reveal a conserved calcium-binding site important for LapG function.
Predictive strategies for low-power RTOS scheduling

Limiting the power consumption of real time embedded systems is an important aspect, especially in portable systems (laptops, cellular phones) with tight power constraints. In this paper, we present a power-saving prediction strategy that exploits the fixed priority scheduling of the real-time tasks running on these embedded systems. Power reduction is achieved by developing an efficient low power scheme with prediction of the expected execution time of real time tasks and making use of the idle time of system for scheduling these tasks in low power modes. In the process there may be few tasks missing their deadlines. This results in a tradeoff between power saved and deadlines missed. Our simulation results for different applications show that the proposed prediction mechanism achieves a high degree of power conservation with a very small penalty of missed deadlines. Our mechanism is simple and can be implemented in most of the real time operating systems.
Extracting 3D Parametric Curves from 2D Images of Helical Objects

Helical objects occur in medicine, biology, cosmetics, nanotechnology, and engineering. Extracting a 3D parametric curve from a 2D image of a helical object has many practical applications, in particular being able to extract metrics such as tortuosity, frequency, and pitch. We present a method that is able to straighten the image object and derive a robust 3D helical curve from peaks in the object boundary. The algorithm has a small number of stable parameters that require little tuning, and the curve is validated against both synthetic and real-world data. The results show that the extracted 3D curve comes within close Hausdorff distance to the ground truth, and has near identical tortuosity for helical objects with a circular profile. Parameter insensitivity and robustness against high levels of image noise are demonstrated thoroughly and quantitatively.
Predictors of Serum Vitamin D Levels in African American and European American Men in Chicago

Vitamin D deficiency is epidemiologically linked to prostate, breast, and colon cancer. When compared with European American (EA) men, African American (AA) men have increased risk of prostate cancer, but few studies evaluate vitamin D status in AA men. The authors evaluate the biological and environmental predictors of vitamin D deficiency in AA and EA men in Chicago, Illinois, a low ultraviolet radiation environment. Blood samples were collected from 492 men, aged between 40 and 79 years, from urology clinics at three hospitals in Chicago, along with demographic and medical information, body mass index, and skin melanin content using a portable narrow-band reflectometer. Vitamin D intake and ultraviolet radiation exposure were assessed using validated questionnaires. The results demonstrated that Black race, cold season of blood draw, elevated body mass index, and lack of vitamin D supplementation increase the risk of vitamin D deficiency. Supplementation is a high-impact, modifiable risk factor. Race and sunlight exposure should be taken into account for recommended daily allowances for vitamin D intake.
Principal Graph and Structure Learning Based on Reversed Graph Embedding

Many scientific datasets are of high dimension, and the analysis usually requires retaining the most important structures of data. Principal curve is a widely used approach for this purpose. However, many existing methods work only for data with structures that are mathematically formulated by curves, which is quite restrictive for real applications. A few methods can overcome the above problem, but they either require complicated human-made rules for a specific task with lack of adaption flexibility to different tasks, or cannot obtain explicit structures of data. To address these issues, we develop a novel principal graph and structure learning framework that captures the local information of the underlying graph structure based on reversed graph embedding. As showcases, models that can learn a spanning tree or a weighted undirected `1 graph are proposed, and a new learning algorithm is developed that learns a set of principal points and a graph structure from data, simultaneously. The new algorithm is simple with guaranteed convergence. We then extend the proposed framework to deal with large-scale data. Experimental results on various synthetic and six real world datasets show that the proposed method compares favorably with baselines and can uncover the underlying structure correctly.
Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2

ABSTRACT While SecA is the ATPase component of the major bacterial secretory (Sec) system, mycobacteria and some Gram-positive pathogens have a second paralog, SecA2. In bacteria with two SecA paralogs, each SecA is functionally distinct, and they cannot compensate for one another. Compared to SecA1, SecA2 exports a distinct and smaller set of substrates, some of which have roles in virulence. In the mycobacterial system, some SecA2-dependent substrates lack a signal peptide, while others contain a signal peptide but possess features in the mature protein that necessitate a role for SecA2 in their export. It is unclear how SecA2 functions in protein export, and one open question is whether SecA2 works with the canonical SecYEG channel to export proteins. In this study, we report the structure of Mycobacterium tuberculosis SecA2 (MtbSecA2), which is the first structure of any SecA2 protein. A high level of structural similarity is observed between SecA2 and SecA1. The major structural difference is the absence of the helical wing domain, which is likely to play a role in how MtbSecA2 recognizes its unique substrates. Importantly, structural features critical to the interaction between SecA1 and SecYEG are preserved in SecA2. Furthermore, suppressor mutations of a dominant-negative secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG or the translocating polypeptide substrate. These results support a model in which the mycobacterial SecA2 works with SecYEG. IMPORTANCE SecA2 is a paralog of SecA1, which is the ATPase of the canonical bacterial Sec secretion system. SecA2 has a nonredundant function with SecA1, and SecA2 exports a distinct and smaller set of substrates than SecA1. This work reports the crystal structure of SecA2 of Mycobacterium tuberculosis (the first SecA2 structure reported for any organism). Many of the structural features of SecA1 are conserved in the SecA2 structure, including putative contacts with the SecYEG channel. Several structural differences are also identified that could relate to the unique function and selectivity of SecA2. Suppressor mutations of a secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG.
Role of RNase Y in Clostridium perfringens mRNA Decay and Processing

ABSTRACT RNase Y is a major endoribonuclease that plays a crucial role in mRNA degradation and processing. We study the role of RNase Y in the Gram-positive anaerobic pathogen Clostridium perfringens, which until now has not been well understood. Our study implies an important role for RNase Y-mediated RNA degradation and processing in virulence gene expression and the physiological development of the organism. We began by constructing an RNase Y conditional knockdown strain in order to observe the importance of RNase Y on growth and virulence. Our resulting transcriptome analysis shows that RNase Y affects the expression of many genes, including toxin-producing genes. We provide data to show that RNase Y depletion repressed several toxin genes in C. perfringens and involved the virR-virS two-component system. We also observe evidence that RNase Y is indispensable for processing and stabilizing the transcripts of colA (encoding a major toxin collagenase) and pilA2 (encoding a major pilin component of the type IV pili). Posttranscriptional regulation of colA is known to be mediated by cleavage in the 5′ untranslated region (5′UTR), and we observe that RNase Y depletion diminishes colA 5′UTR processing. We show that RNase Y is also involved in the posttranscriptional stabilization of pilA2 mRNA, which is thought to be important for host cell adherence and biofilm formation. IMPORTANCE RNases have important roles in RNA degradation and turnover in all organisms. C. perfringens is a Gram-positive anaerobic spore-forming bacterial pathogen that produces numerous extracellular enzymes and toxins, and it is linked to digestive disorders and disease. A highly conserved endoribonuclease, RNase Y, affects the expression of hundreds of genes, including toxin genes, and studying these effects is useful for understanding C. perfringens specifically and RNases generally. Moreover, RNase Y is involved in processing specific transcripts, and we observed that this processing in C. perfringens results in the stabilization of mRNAs encoding a toxin and bacterial extracellular apparatus pili. Our study shows that RNase activity is associated with gene expression, helping to determine the growth, proliferation, and virulence of C. perfringens.