Miracle-dz/UniFAR-FTUs huggingface dataset:
The crystal structure of the penicillin-binding protein 2x from Streptococcus pneumoniae and its acyl-enzyme form: implication in drug resistance.

Penicillin-binding proteins (PBPs), the primary targets for beta-lactam antibiotics, are periplasmic membrane-attached proteins responsible for the construction and maintenance of the bacterial cell wall. Bacteria have developed several mechanisms of resistance, one of which is the mutation of the target enzymes to reduce their affinity for beta-lactam antibiotics. Here, we describe the structure of PBP2x from Streptococcus pneumoniae determined to 2.4 A. In addition, we also describe the PBP2x structure in complex with cefuroxime, a therapeutically relevant antibiotic, at 2.8 A. Surprisingly, two antibiotic molecules are observed: one as a covalent complex with the active-site serine residue, and a second one between the C-terminal and the transpeptidase domains. The structure of PBP2x reveals an active site similar to those of the class A beta-lactamases, albeit with an absence of unambiguous deacylation machinery. The structure highlights a few amino acid residues, namely Thr338, Thr550 and Gln552, which are directly related to the resistance phenomenon.
The development of nano-structured plasmonic composite by two-step ion-exchange processes

Surface enhanced Raman scattering (SERS) active substrate was fabricated using Ag+-Na+ ion-exchange technique. A thin layer of Aluminum was subsequently deposited which provides electrons and effectively promotes the reduction of the Ag+ ions in the follow-up Na+-K+ ion exchange process. The extinction spectrum exhibits a broadened and red-shifted peak indicating that the filling fraction was increased, and the distribution of the particle size and shape are multi-dispersed. The trend can be explained by Maxwell Garnett theory enabling molecular sensing over a wide spectral range. The spectral fingerprint of Rhodamine 6G molecules is successfully detected in the Raman spectrum.
Interference cancellation with an achievable angular channel model based on Coordinate Multi-Point

Latterly, interference cancellation is a hard issue in cellular systems. Hence we present interference cancellation with an achievable angular channel model based on Coordinated Multi-Point (CoMP) system in our paper. The CoMP schemes are adopted by Long Term Evolution-Advanced (LTE-A) to enhance the LTE downlink data rate, spectral efficiency, average cell throughput etc. This paper inquires about the performance of CoMP and estimates an achievable angular channel model for LTE-A using minimum mean square error (MMSE) receiver which efficiently improves the bit-error-rate (BER) and cell-edge throughput per user.
Optimization based on genetic algorithm and HFSS and its application to the semiautomatic design of antenna

In this paper, a technique based on the combination of genetic algorithm (GA) with high frequency simulation software (HFSS) is presented to perform optimization. The technique is realized by MATLAB and VB script of HFSS. Then, the technique is used to guide the design and optimization of broadband microstrip antenna. The feasibility of the technique is validated by the example.
A new method for isolating colonocytes from naturally evacuated feces and its clinical application to colorectal cancer diagnosis.

BACKGROUND & AIMS The early detection of colorectal cancer is desired because this cancer can be cured surgically if diagnosed early. The purpose of the present study was to determine the feasibility of a new methodology for isolating colonocytes from naturally evacuated feces, followed by cytology or molecular biology of the colonocytes to detect colorectal cancer originating from any part of the colorectum. METHODS Several simulation studies were conducted to establish the optimal methods for retrieving colonocytes from any portion of feces. Colonocytes exfoliated into feces, which had been retrieved from 116 patients with colorectal cancer and 83 healthy volunteers, were analyzed. Part of the exfoliated colonocytes was examined cytologically, whereas the remainder was subjected to DNA analysis. The extracted DNA was examined for mutations of the APC, K-ras, and p53 genes using direct sequence analysis and was also subjected to microsatellite instability (MSI) analysis. RESULTS In the DNA analysis, the overall sensitivity and specificity were 71% (82 of 116) of patients with colorectal cancer and 88% (73 of 83) of healthy volunteers. The sensitivity for Dukes A and B was 72% (44 of 61). Furthermore, the sensitivity for cancers on the right side of the colon was 57% (20 of 35). The detection rate for genetic alterations using our methodology was 86% (80 of 93) when the analysis was limited to cases in which genetic alterations were present in the cancer tissue. CONCLUSIONS We have developed a new methodology for isolating colonocytes from feces. The present study describes a promising procedure for future clinical evaluations and the early detection of colorectal cancers, including right-side colon cancer.
Direct binding of GABAA receptor β2 and β3 subunits to gephyrin

GABAergic transmission is essential to brain function, and a large repertoire of GABA type A receptor (GABAAR) subunits is at a neuron's disposition to serve this function. The glycine receptor (GlyR)‐associated protein gephyrin has been shown to be essential for the clustering of a subset of GABAAR. Despite recent progress in the field of gephyrin‐dependent mechanisms of postsynaptic GABAAR stabilisation, the role of gephyrin in synaptic GABAAR localisation has remained a complex matter with many open questions. Here, we analysed comparatively the interaction of purified rat gephyrin and mouse brain gephyrin with the large cytoplasmic loops of GABAAR α1, α2, β2 and β3 subunits. Binding affinities were determined using surface plasmon resonance spectroscopy, and showed an ~ 20‐fold lower affinity of the β2 loop to gephyrin as compared to the GlyR β loop–gephyrin interaction. We also probed in vivo binding in primary cortical neurons by the well‐established use of chimaeras of GlyR α1 that harbour respective gephyrin‐binding motifs derived from the different GABAAR subunits. These studies identify a novel gephyrin‐binding motif in GABAAR β2 and β3 large cytoplasmic loops.
Oral immunization of mice against candidiasis.

Oral immunization with live Candida albicans evoked antibody- and cell-mediated immune responses in gnotobiotic C.B-17 and BALB/c mice. No deaths or systemic candidiasis of endogenous origin were evident in these C. albicans-colonized (pure culture) mice. Histologic examination showed minimal to no infection of the stomach, esophagus, or tongue by C. albicans. Not only were orally immunized mice more resistant to systemic candidiasis (intravenous challenge) than were germfree (nonimmunized) controls, but immunity could be transferred to susceptible mice with immune spleen cells. Oral immunization elicited a Th1-type response in spleen cells and a Th2 response in Peyer's patch lymphocytes. The alimentary tracts of these orally immunized mice remained chronically colonized with C. albicans in spite of the presence of both antibody- and cell-mediated immune responses to C. albicans.
O Sinaes como Sistema

O artigo descreve os principios, as diretrizes, as caracteristicas, os instrumentos, os agentes e os principais procedimentos operacionais do novo Sistema Nacional de Avaliacao da Educacao Superior brasileira (Sinaes). O texto argumenta, entre outros, que o Sinaes se constitui efetivamente como um Sistema, pois integra nao so espacos avaliativos dentro do Ministerio da Educacao (MEC) e os organiza em torno de uma concepcao unica, em estreita vinculacao com as politicas para a educacao superior, como tambem integra os instrumentos de avaliacao entre si, ao mesmo tempo que os integra aos instrumentos de informacao (censo da educacao superior, cadastro de docentes, cadastro de instituicoes e cursos etc.). Esta visao sistemica da avaliacao permite a geracao, a gestao e a disseminacao de indicadores e informacoes de grande interesse para as instituicoes, os cursos, os avaliadores e para a sociedade em geral.
A Survey on Call Admission Control and Bandwidth Allocation for WiMAX

Wimax (IEEE 802.16) is a broadband technology in which service provider features have the ability to maximize air link utilization and system throughput. To attain Quality of Service (QoS), Call Admission Call schemes (CAC) and Bandwidth allocation mechanisms are important due to random variation of channel conditions and user demands. In this work several bandwidth allocation and CAC mechanisms are analysed based on queue size for the constant bit rate and variable bit rate data types.
COURAGE or FAME…? Who should have percutaneous coronary intervention in stable coronary artery disease?

A patient has just been diagnosed with stable coronary artery disease (CAD) and turns to the doctor and asks ‘Do I need a stent for this doctor? ’ The answer, based on current evidence, is not simple. First, there is poor appreciation among clinicians and among patients about the relatively benign prognosis in stable CAD. For example, in the 3825 patients with stable symptomatic CAD in the A Coronary Disease Trial Investigating Outcome with Nifedipine (ACTION) trial there were 1.5 deaths per 100 patient-years at risk and 1.4 myocardial infarctions (MI). 1 Furthermore, the use of statins (62%), ACE inhibitors or angiotensin II receptor blockers (ARB) and other secondary prevention measures did not achieve the levels attained in the subsequent COURAGE trial (95% on statins at 1 year, 95% on aspirin, 89% on beta blockers, 72% on ACE or ARB). 2 However, the overall figure masks a 10-fold range in risk, determined by concomitant risk factors including the extent of coronary disease3 (figure 1). So, the first response to the patient is reassuring; unless there are additional risk factors, the risks of death are relatively low and are reduced by secondary prevention treatments and lifestyle measures including smoking cessation. Figure 1 Impact of underlying risk on probability of death or myocardial infarction (MI) or stroke within 5 years in patients with stable ischaemic heart disease. (Principally: age, ejection fraction, diabetes, smoking, previous MI, renal dysfunction, extent of coronary disease, hypertension, no lipid-lowering therapy). 3 The next question from the patient is ‘Okay, I will take the treatments you prescribe for preventing complications and do my best to adopt the lifestyle changes, but would I be better off with stent therapy? ’ If the patient is symptomatic and is not controlled or is inadequately controlled on anti-anginal medications (because of troublesome angina or side effects) then …
he human milk microbiota : Origin and potential roles in health and disease

Human milk has been traditionally considered sterile; however, recent studies have shown that it represents a continuous supply of commensal, mutualistic and/or potentially probiotic bacteria to the infant gut. Culture-dependent and -independent techniques have revealed the dominance of staphylococci, streptococci, lactic acid bacteria and bifidobacteria in this biological fluid, and their role on the colonization of the infant gut. These bacteria could protect the infant against infections and contribute to the maturation of the immune system, among other functions. Different studies suggest that some bacteria
How Many Butterflies Are There in a City of Circa Half a Million People

Urbanization poses severe threats to biodiversity; thus, there is an urge to understand urban areas and their biological, physical, and social components if we aim to integrate sustainable practices as part of their processes. Among urban wildlife groups, butterflies have been used as biological indicators due to their high sensitivity to environmental changes. In this study, we estimated the number of butterflies that live within a neotropical medium-sized city (Xalapa, Veracruz, Mexico) using a robust interpolation procedure (ordinary kriging). Our calculations added an average of 1,077,537 (± SE 172) butterfly individuals that dwelt in Xalapa in the surveyed space and time. The interpolation procedures showed to be robust and reliable, and up to some extent conservative. Thus, our results suggest that there are at least 1.8 butterfly individuals per capita in Xalapa. Notably, higher butterfly abundances tended to be recorded near highly vegetated areas and along city borders. Besides providing the basis for further ecological studies, our results will contribute to the crucial need of scientific data that is lacking, but critically important, for adequate urban management and planning, as well as environmental education.
Quantitative Proteomic Analysis of Formalin-fixed and Paraffin-embedded Nasopharyngeal Carcinoma Using iTRAQ Labeling, Two-dimensional Liquid Chromatography, and Tandem Mass Spectrometry

Formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a potentially valuable resource for protein biomarker investigations. In this study, proteins were extracted by a heat-induced antigen retrieval technique combined with a retrieval solution containing 2% SDS from FFPE tissues of normal nasopharyngeal epithelial tissues (NNET) and three histological types of nasopharyngeal carcinoma (NPC) with diverse differentiation degrees. Then two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification (iTRAQ) labeling was employed to quantitatively identify the differentially expressed proteins among the types of NPC FFPE tissues. Our study resulted in the identification of 730 unique proteins, the distributions of subcellular localizations and molecular functions of which were similar to those of the proteomic database of human NPC and NNET that we had set up based on the frozen tissues. Additionally, the relative expression levels of cathepsin D, keratin8, SFN, and stathmin1 identified and quantified in this report were consistent with the immunohistochemistry results acquired in our previous study. In conclusion, we have developed an effective approach to identifying protein changes in FFPE NPC tissues utilizing iTRAQ technology in conjunction with an economical and easily accessible sample preparation method.
Case ascertainment in pediatric traumatic brain injury: Challenges in using the NEISS

Primary objective: To evaluate mild traumatic brain injury (TBI) case ascertainment in the US National Electronic Injury Surveillance System (NEISS). Research design: A sample of NEISS injury cases was analyzed. Two trained researchers independently reviewed diagnostic codes based on the International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM). The sensitivity and specificity of two NEISS TBI definitions were evaluated, and Kappa coefficients were calculated to evaluate the agreement between NEISS TBI definitions and the standard TBI definition based on the ICD-9-CM. Results: Our sampling procedures provided a total of 1,018 NEISS cases, of which 880 were injury cases and 138 were non-injury cases. Out of the injury cases, 54 cases were defined as mild TBI cases based on the ICD-9-CM diagnosis codes. Compared with non-TBI injury cases, a significantly higher percentage of TBI cases (33.3% versus 15.4%) were infants less than 1 year old and TBI cases were more likely to be admitted for hospitalization. If TBI was identified using NEISS definition 1 (diagnosis code 52 for ‘concussion’), the sensitivity was only 38.9% (95% confidence intervals (CI) = 25.9–51.9%). However, if TBI was identified using NEISS definition 2 (diagnosis code 52 for ‘concussion’ or 62 for ‘internal organ injury’ and ‘head’ was the affected body part), the sensitivity increased dramatically to 79.6% (95% CI = 68.9–90.4%). The Kappa coefficient for overall agreement between the NEISS and ICD-9-CM system was 0.528 (95% CI = 0.393–0.664) for NEISS definition 1 and 0.807 (95% CI = 0.723–0.892) for NEISS definition 2. Conclusions: The current approach of pediatric TBI case ascertainment in the NEISS faces some challenges in identifying mild TBI. Future research efforts are needed to refine TBI case ascertainment in the NEISS.
Growth, grazing and carbon flux of high and low nucleic acid bacteria differ in surface and deep chlorophyll maximum layers in the NW Mediterranean Sea

Growth and grazing mortality of marine heterotrophic bacteria were measured in the summer of 2000 in coastal waters of the NW Mediterranean Sea. Serial-dilution experiments were performed with water from surface and deep chlorophyll maximum (DCM) layers. Bacterial abun- dances (mean ± SD) were very similar at the surface (7.2 ± 2.9 × 10 5 cells ml -1 ) and DCM (7.4 ± 1.1 × 10 5 cells ml -1 ). Intrinsic bacterial growth rates (mean ± SD) were 0.88 ± 0.43 d -1 in the surface layer and 0.71 ± 0.23 d -1 at the DCM. Grazing rates on bacteria (mean ± SD) were 0.75 ± 0.23 and 0.58 ± 0.29 d -1 , in the surface and DCM layers, respectively. Nucleic acid content analysis by flow cytometry revealed different intrinsic growth rates and grazing pressure on bacteria of high (HNA) and low (LNA) content depending on their location in the water column. Generally, growth and grazing rates were balanced in both groups in both layers. At the surface, HNA bacteria revealed significantly higher intrinsic growth rates than LNA bacteria (1.18 ± 0.60 and 0.47 ± 0.28 d -1 , respectively). Aver- age growth rates at the DCM were higher for LNA (0.90 ± 0.46 d -1 ) than for HNA (0.36 ± 0.23 d -1 ), but not significantly. At the surface, grazing rates on HNA bacteria were also significantly higher than on LNA bacteria (1.02 ± 0.31 and 0.37 ± 0.19 d -1 , respectively). At the DCM, the opposing tendency, though not statistically significant, was observed (0.26 ± 0.17 and 0.77 ± 0.50 d -1 ). Bacteria were responsible for a large portion of the C flux through the system. Bacterial C flux was funneled mostly by HNA bacteria at the surface (70%) and by LNA at the DCM (80%). HNA bacteria were the most active component of the bacterial community in the surface layer. However, we found that LNA bac- teria were also active, particularly at the DCM, suggesting differences in structure and functioning of the corresponding microbial networks. The most significant result was the clear relation between depth and activity of each bacterial fraction.
Observability and Performance Analysis of Bi/Multi-Static Doppler-Only Radar

Bi/multi-static radars using cooperative or noncooperative transmitters have attracted wide attention. This paper analyzes the method of locating a moving target from corrupted Doppler frequency measurements obtained by single or multiply receivers located together and with corresponding cooperative or noncooperative transmitters distributing in remote places. Both the observability requirements in two dimensions and the expressions for the Cramér-Rao bound are derived. Further analysis with simulation results reveals the relationship between the performance and the number of transmitters and the sensitivity between the performance and the time integration. It is shown that the bi/multi-static radars can exploit only Doppler information to locate a moving target effectively.
Ocular disease leads to decreased concentrations of epidermal growth factor in the tear fluid.

The concentration of epidermal growth factor (EGF) in tear fluid (TF) was recently shown to decrease with increasing tear fluid flow (TFF). The purpose of the present study was to clarify the effects of ocular surface disease on the TF EGF concentrations. Tear fluid samples (n = 243) were collected from diseased eyes by means of blunted glass capillaries. The time of collection was measured for each sample, and the tear fluid flow in the capillaries (TFFc) was calculated. The concentration of human EGF (hEGF) was determined using a time-resolved immunofluorometric assay (TR-IFMA). For statistical analysis diagnosis-dependent multigrouping was performed and the data of the patient groups were compared to the data for a control group. The control material consisted of 271 TF samples collected from healthy eyes before (n = 59) and after stimulation of reflex tearing (n = 212). It was shown that TF specimens of patients (n = 243) contained significantly (p less than 0.001) less EGF (mean 952 pg/ml) than the TF of healthy control individuals before (n = 59 samples; mean 6589 pg/ml) or after stimulation of reflex tearing (n = 212 samples; mean 2762 pg/ml). The EGF concentration of every patient group was significantly lower than that found in the TF of control individuals both before and during reflex tearing (p less than 0.001). The rate of EGF released with TF during collection did not differ significantly between the various groups of patients or from that released with the TF of normal individuals before induction of reflex tearing. (ABSTRACT TRUNCATED AT 250 WORDS)
New Practical Algebraic Public-Key Cryptosystem and Some Related Algebraic and Computational Aspects

The most popular present-day public-key cryptosystems are RSA and ElGamal cryptosystems. Some practical algebraic generalization of the ElGamal cryptosystem is considered-basic modular matrix cryptosystem (BMMC) over the modular matrix ring M2(Zn). An example of computation for an artificially small number n is presented. Some possible attacks on the cryptosystem and mathematical problems, the solution of which are necessary for implementing these attacks, are studied. For a small number n, computational time for compromising some present-day public-key cryptosystems such as RSA, ElGamal, and Rabin, is compared with the corresponding time for the ВММС. Finally, some open mathematical and computational problems are formulated.
Reproductive skew among males in a female-dominated mammalian society

The purpose of this study was to document patterns of reproductive skew among male spotted hyenas (Crocuta crocuta), a species in which many normal mammalian sex roles are reversed. We used paternity determined from 12 microsatellite markers together with demographic and behavioral data collected over 10 years from a free-living population to document relationships among reproductive success (RS), social rank, and dispersal status of male hyenas. Our data suggest that dispersal status and length of residence are the strongest determinants of RS. Natal males comprise over 20% of the adult male population, yet they sire only 3% of cubs, whereas immigrants sire 97%. This reproductive advantage to immigrants accrues despite the fact that immigrants are socially subordinate to all adult natal males, and it provides a compelling ultimate explanation for primary dispersal in this species. High-ranking immigrants do not monopolize reproduction, and tenure accounts for more of the variance in male reproductive success than does social rank. Immigrant male hyenas rarely fight among themselves, so combat between rivals may be a relatively ineffectual mode of sexual selection in this species. Instead, female choice of mates appears to play an important role in determining patterns of paternity in Crocuta. Our data support a ‘‘limited control’’ model of reproductive skew in this species, in which female choice may play a more important role in limiting control by dominant males than do power struggles among males. Key words: Crocuta, dispersal, hyena, mate choice, rank, reproductive skew, reproductive success, tenure. [Behav Ecol 13:193–200 (2002)]