Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Characterization and Physiological Role of Endopeptidase O from Lactobacillus helveticus CNRZ32

ABSTRACT A previously identified insert expressing an endopeptidase from aLactobacillus helveticus CNRZ32 genomic library was characterized. Nucleotide sequence analysis revealed an open reading frame of 1,941 bp encoding a putative protein of 71.2 kDa which contained a zinc-protease motif. Protein homology searches revealed that this enzyme has 40% similarity with endopeptidase O (PepO) fromLactococcus lactis P8-2-47. Northern hybridization revealed that pepO is monocistronic and is expressed throughout the growth phase. CNRZ32 derivatives lacking PepO activity were constructed via gene replacement. Enzyme assays revealed that the PepO mutant had significantly reduced endopeptidase activity when compared to CNRZ32 with two of the three substrates examined. Growth studies indicated that PepO has no detectable effect on growth rate or acid production by Lactobacillus helveticusCNRZ32 in amino acid defined or skim milk medium.
Functional Gait Adaptations in Patients With Anterior Cruciate Ligament Deficiency Over Time

Functional adaptations in knee kinematics and kinetics during level walking in 30 patients with unilateral anterior cruciate ligament deficiency and 30 healthy control subjects were studied. To examine the impact of time after injury on the functional adaptations, patients were placed into three time interval groups: early, intermediate, and chronic. The patients with anterior cruciate ligament deficiency had significantly decreased external knee flexion moments (balanced by net quadriceps contraction) and significantly increased external knee extension moments (balanced by net knee flexors contraction) as compared with the control subjects. As time after the injury increased, changes in the sagittal plane knee moments were more pronounced. A significant linear relationship (positive correlation) was found between the midstance knee flexion moment and the corresponding knee flexion angle. The patients with anterior cruciate deficiency had a greater knee flexion angle when generating a comparable midstance knee flexion moment as compared to the control subjects. The identification of gait adaptations over time provides additional information on the natural history of anterior cruciate ligament deficiency and may have implications regarding conservative rehabilitation, evaluation of outcomes, progression of meniscal injury, and the development of degenerative arthritis of the knee.
Early Identification of Acute Kidney Injury after Bariatric Surgery: Role of NGAL and Cystatin C

Background: The aim of our study was to evaluate plasmatic and urinary NGAL and serum cystatin C as early diagnostic markers of acute kidney injury in obese patients undergoing bariatric surgery. Methods: For this this prospective observational study, we recruited 23 patients undergoing gastric by-pass or sleeve gastrectomy, and admitted to the Low Dependence Unit after the surgery. Plasma NGAL (pNGAL), urinary NGAL (uNGAL), serum cystatin C, serum creatinine, and serum urea were measured before surgery as well as 10 h and 24 h after surgery. Mean values of pNGAL, uNGAL, cystatin C, creatinine, and urea concentrations of pre- and post-surgery periods were compared using Student's t test for paired data. We also evaluated the presence of correlation between modifications of NGAL and cystatin C after surgery and fluid balance, hydration (ml/kg) and diuresis using Pearson's coefficient of correlation. Results: No patient developed AKI according to the AKIN criteria. pNGAL was significantly higher at T10h than T0 (p=0.004). There was no significant difference between uNGAL at T0 and T10h (p=0.53) and between uNGAL at T0 and T24h (p=0.31). uNGAL at T24h was significantly higher in comparison to T10h (p=0.024). uNGAL concentrations were normal in all patients at every time step. Cystatin C concentration did not increase after surgery. Serum creatinine level was significantly higher at T48h, despite being still within the normal range, when compared to T0 (p=0.038). Conclusion: Our study shows that pNGAL can reflect mild tubular damage as its levels increase within a few hours from surgery and return to normal limits afterwards. Concerning uNGAL, there is a minimal increase at T24h, when NGAL concentration in plasma has already decreased. Serum cystatin C does not show any relevant kidney changes, or at least, no more than those ones shown by pNGAL.
Low Noise Amplification at 0.67 THz Using 30 nm InP HEMTs

In this letter, low noise amplification at 0.67 THz is demonstrated for the first time. A packaged InP High Electron Mobility Transistor (HEMT) amplifier is reported to achieve a noise figure of 13 dB with an associated gain greater than 7 dB at 670 GHz using a high fMAX InP HEMT transistors in a 5 stage coplanar waveguide integrated circuit. A 10-stage version is also reported to reach a peak gain of 30 dB. These results indicate that InP HEMT integrated circuits can be useful at frequencies approaching a terahertz.
Studies on the substrate specificity of human and pig lecithin: cholesterol acyltransferase: role of low-density lipoproteins.

The substrate properties of low-density lipoprotein (LDL) fractions from human and pig plasma and of lipoprotein a [Lp(a)] upon incubation with either pig or human lecithin:cholesterol acyltransferase (LCAT, EC 2.3.1.43) were investigated and compared with those of pig high-density lipoproteins (HDL) or human HDL-3. The cholesterol esterification using purified native pig LDL-1, human LDL, or Lp(a) as a substrate was approximately 36-42% that of pig HDL or human HDL-3, while cholesteryl ester formation with pig LDL-2 was 41-47%. No significant difference was found in the substrate activity between pig HDL and human HDL-3, and between human LDL and Lp(a), respectively. After depletion of pig LDL-1, pig LDL-2, and human LDL from apolipoprotein A-I (apoA-I), cholesteryl ester formation decreased to about 22-28% of the value found with pig HDL. Depletion of human LDL from apolipoprotein E (apoE) did not result in significantly different esterification rates in comparison to native LDL. Total removal of non-apoB proteins from human LDL resulted in esterification rates of approximately 10-15% that of HDL. Readdition of apoA-I to all these LDL fractions produced solely in apoA-I-depleted LDL fractions an increase of cholesteryl ester formation, whereas in those LDL fractions that were additionally depleted from apoE and/or from apoC polypeptides, a further decrease in the esterification rate occurred. (ABSTRACT TRUNCATED AT 250 WORDS)
Idiom recognition in the Polaris parallelizing compiler

The elimination of induction variables and the parallelization of reductions in FORTRAN programs have been shown to be integral to performance improvement on parallel computers [7, 8]. As part of the Polaris project [5], compiler passes that recognize these idioms have been implemented and evaluated. Developing these techniques to the point necessary to achieve signi cant speedups on real applications has prompted solutions to problems that have not been addressed in previous reports on idiom recognition techniques. These include analysis techniques capable of disproving zero-trip loops, symbolic handling facilities to compute closed forms of recurrences, and interfaces to other compilation passes such as the data-dependence test. In comparison, the recognition phase of solving induction variables, which has receivedmost attention so far, has in fact turned out to be relatively straightforward. This paper provides an overview of techniques described in more detail in [12].
Efficient discriminative learning of parametric nearest neighbor classifiers

Linear SVMs are efficient in both training and testing, however the data in real applications is rarely linearly separable. Non-linear kernel SVMs are too computationally intensive for applications with large-scale data sets. Recently locally linear classifiers have gained popularity due to their efficiency whilst remaining competitive with kernel methods. The vanilla nearest neighbor algorithm is one of the simplest locally linear classifiers, but it lacks robustness due to the noise often present in real-world data. In this paper, we introduce a novel local classifier, Parametric Nearest Neighbor (P-NN) and its extension Ensemble of P-NN (EP-NN). We parameterize the nearest neighbor algorithm based on the minimum weighted squared Euclidean distances between the data points and the prototypes, where a prototype is represented by a locally linear combination of some data points. Meanwhile, our method attempts to jointly learn both the prototypes and the classifier parameters discriminatively via max-margin. This makes our classifiers suitable to approximate the classification decision boundaries locally based on nonlinear functions. During testing, the computational complexity of both classifiers is linear in the product of the dimension of data and the number of prototypes. Our classification results on MNIST, USPS, LETTER, and Chars 74K are comparable and in some cases are better than many other methods such as the state-of-the-art locally linear classifiers.
Effect of Flood Hydrograph Duration, Magnitude, and Shape on Bed Load Transport Dynamics

Bed load sediment transport is an inherently challenging process to measure within a river, which is further complicated by the typically transient nature of the hydrograph. Here we use laboratory experiments to explore how sediment flux under transient—unsteady and intermittent—flow differ from those under steady flow. For a narrow unimodal sediment distribution, we calculated fluid stress and measured sediment flux for a range of hydrograph durations, magnitudes, shapes, and sequences. Within a hydrograph, we find considerable variability in sediment flux for a given stress above the threshold for motion. However, cumulative bed load flux resulting from a flood scales linearly with the integrated excess transport capacity (flow impulse). This scaling indicates that, to first order, flow magnitude, duration, shape, and sequence are only relevant to bed load flux in terms of their contribution to the total flow impulse, in agreement with prior field results. The flood impulse represents a quantitative parameter through which the effects of transient flow on coarse sediment transport may be parsed.
On the evolution of elastic properties during laboratory stick‐slip experiments spanning the transition from slow slip to dynamic rupture

The physical mechanisms governing slow earthquakes remain unknown, as does the relationship between slow and regular earthquakes. To investigate the mechanism(s) of slow earthquakes and related quasi‐dynamic modes of fault slip we performed laboratory experiments on simulated fault gouge in the double direct shear configuration. We reproduced the full spectrum of slip behavior, from slow to fast stick slip, by altering the elastic stiffness of the loading apparatus (k) to match the critical rheologic stiffness of fault gouge (kc). Our experiments show an evolution from stable sliding, when k > kc, to quasi‐dynamic transients when k ~ kc, to dynamic instabilities when k < kc. To evaluate the microphysical processes of fault weakening we monitored variations of elastic properties. We find systematic changes in P wave velocity (Vp) for laboratory seismic cycles. During the coseismic stress drop, seismic velocity drops abruptly, consistent with observations on natural faults. In the preparatory phase preceding failure, we find that accelerated fault creep causes a Vp reduction for the complete spectrum of slip behaviors. Our results suggest that the mechanics of slow and fast ruptures share key features and that they can occur on same faults, depending on frictional properties. In agreement with seismic surveys on tectonic faults our data show that their state of stress can be monitored by Vp changes during the seismic cycle. The observed reduction in Vp during the earthquake preparatory phase suggests that if similar mechanisms are confirmed in nature high‐resolution monitoring of fault zone properties may be a promising avenue for reliable detection of earthquake precursors.
Identification of Protein Complexes Using Weighted PageRank-Nibble Algorithm and Core-Attachment Structure

Protein complexes play a significant role in understanding the underlying mechanism of most cellular functions. Recently, many researchers have explored computational methods to identify protein complexes from protein-protein interaction (PPI) networks. One group of researchers focus on detecting local dense subgraphs which correspond to protein complexes by considering local neighbors. The drawback of this kind of approach is that the global information of the networks is ignored. Some methods such as Markov Clustering algorithm (MCL), PageRank-Nibble are proposed to find protein complexes based on random walk technique which can exploit the global structure of networks. However, these methods ignore the inherent core-attachment structure of protein complexes and treat adjacent node equally. In this paper, we design a weighted PageRank-Nibble algorithm which assigns each adjacent node with different probability, and propose a novel method named WPNCA to detect protein complex from PPI networks by using weighted PageRank-Nibble algorithm and core-attachment structure. Firstly, WPNCA partitions the PPI networks into multiple dense clusters by using weighted PageRank-Nibble algorithm. Then the cores of these clusters are detected and the rest of proteins in the clusters will be selected as attachments to form the final predicted protein complexes. The experiments on yeast data show that WPNCA outperforms the existing methods in terms of both accuracy and p-value.The software for WPNCA is available at “http://netlab.csu. edu.cn/bioinfomatics/weipeng/WPNCA/download.html”.
Extremely low frequency‐modulated static magnetic fields to treat cancer: A pilot study on patients with advanced neoplasm to assess safety and acute toxicity

Results of a toxicity pilot human study approved by the competent ethical Committee are reported. Eleven patients with heavily pre‐treated advanced cancer were enrolled in a pilot study with different schedules of time exposure to static magnetic fields (MF), amplitude modulated by ELF. An area including the neck, thoracic and abdomen was MF exposed daily, 5 days/week for 4 weeks according to two different schedules: 20 min daily (4 patients) and 70 min daily (7 patients). ECOG performance status was 1 (2 patients), 2 (8 patients), 3 (1 patient). Toxicity was assessed according to WHO criteria. ECG, Chest X‐ray, physical examination, blood cell count and complete blood chemistry were performed before and at the end of the treatment. Aspartate aminotransferase (AST) and alanine aminotransferase (ALT) elevation (grade 2 toxicity) in 1 patient and microscopic urinary abnormalities in 5 patients were the only negative effects observed. We conclude that MF can be safely administrated according to the MF exposure schedules. Bioelectromagnetics 25:563–571, 2004. © 2004 Wiley‐Liss, Inc.
Investigations on Fusarium spp. and their mycotoxins causing Fusarium ear rot of maize in Kosovo

After wheat, maize (Zea mays L.) is the second most important cereal crop in Kosovo and a major component of animal feed. The purpose of this study was to analyse the incidence and identity of the Fusarium species isolated from naturally infected maize kernels in Kosovo in 2009 and 2010, as well as the mycotoxin contamination. The disease incidence of Fusarium ear rot (from 0.7% to 40% diseased ears) on maize in Kosovo is high. The most frequently Fusarium spp. identified on maize kernels were Fusarium subglutinans, F. verticillioides/F. proliferatum and F. graminearum. Maize kernel samples were analysed by LC-MS/MS and found to be contaminated with deoxynivalenol (DON), DON-3-glucoside, 3-acetyl-DON, 15-acetyl-DON, zearalenone, zearalenone-14-sulphate, moniliformin, fumonisin B1 and fumonisin B2. This is the first report on the incidence and identification of Fusarium species isolated from naturally infected maize as well as the mycotoxin contamination in Kosovo.
Gromov-Witten invariants on Grassmannians

We prove that any three-point genus zero Gromov-Witten invariant on a type A Grassmannian is equal to a classical intersection number on a two-step flag variety. We also give symplectic and orthogonal analogues of this result; in these cases the two-step flag variety is replaced by a sub-maximal isotropic Grassmannian. Our theorems are applied, in type A, to formulate a conjectural quantum Littlewood-Richardson rule, and in the other classical Lie types, to obtain new proofs of the main structure theorems for the quantum cohomology of Lagrangian and orthogonal Grassmannians.
Renal accumulation of pentosidine in non-diabetic proteinuria-induced renal damage in rats.

BACKGROUND Advanced glycation end-products (AGEs) contribute to the pathogenesis of diabetic glomerulopathy. The role of AGEs in non-diabetic renal damage is not well characterized. First, we studied whether renal AGE accumulation occurs in non-diabetic proteinuria-induced renal damage and whether this is ameliorated by renoprotective treatment. Secondly, we investigated whether renal AGE accumulation was due to intrarenal effects of local protein trafficking. METHODS Pentosidine was measured (by high-performance liquid chromatography) in rats with chronic bilateral adriamycin nephropathy (AN), untreated and treated with lisinopril. Age-matched healthy rats served as negative controls. Secondly, we compared renal pentosidine in mild proteinuric and non-proteinuric kidneys of unilateral AN and in age-matched controls at 12 and 30 weeks. Intrarenal localization of pentosidine was studied by immunohistochemistry. RESULTS Renal pentosidine was elevated in untreated AN (0.14+/-0.04 micromol/mol valine) vs healthy controls (0.04+/-0.01 micromol/mol valine, P<0.01). In lisinopril-treated AN, pentosidine was lower (0.09+/-0.02 micromol/mol valine) than in untreated AN (P<0.05). In unilateral proteinuria, pentosidine was similar in non-proteinuric and proteinuric kidneys. After 30 weeks of unilateral proteinuria, pentosidine was increased in both kidneys (0.26+/-0.10 micromol/mol valine) compared with controls (0.18+/-0.06 micromol/mol valine, P<0.05). Pentosidine (AN, week 30) was also increased compared with AN at week 12 (0.16+/-0.06 micromol/mol valine, P<0.01). In control and diseased kidneys, pentosidine was present in the collecting ducts. In proteinuric kidneys, in addition, pentosidine was present in the brush border and cytoplasm of dilated tubular structures, i.e. at sites of proteinuria-induced tubular damage. CONCLUSION Pentosidine accumulates in non-diabetic proteinuric kidneys in damaged tubules, and renoprotective treatment by angiotensin-converting enzyme (ACE) inhibitors inhibits AGE accumulation, supporting a relationship between abnormal renal protein trafficking, proteinuria-induced tubular damage and tubular pentosidine accumulation. Future studies, applying specific AGE inhibitors, should be conducted to provide insight into the pathophysiological significance of renal AGEs in non-diabetic renal disease.
Multiple Digital Watermarking Applied to Medical Imaging

Beyond its already established wide range of applications, digital watermarking has recently started to gain a foothold in the healthcare sector. The paper discusses the potential of multiple watermarking to address a number of health information management issues, such as protection of sensitive data, origin and data authentication, image archiving and retrieval. A wavelet-based multiple watermarking scheme focusing on these medical-oriented applications is presented; the scheme allows the physician to define a region of interest, whose diagnostic value is explicitly protected throughout the embedding process, since the only additional information inserted therein is for the purpose of integrity control. The rest part of the image casts multiple watermarks conveying the physician's digital signature, patient's sensitive data, and keywords allowing image retrieval. In order to increase data robustness, a form of hybrid coding is applied, which includes repetitive embedding of BCH encoded watermarks
Genetic polymorphisms associated with steroids metabolism and insulin action in polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is an endocrinopathy associated with infertility, diabetes and cardiovascular events. This study aimed to correlate polymorphisms of genes involved in the biosynthesis and metabolism of steroids and insulin action (CYP17A1, CYP19A1, AR, ESR1, ESR2, INSR, IGF2 and PAI1) with clinical and biochemical parameters of PCOS. DNA was extracted from peripheral blood samples obtained from 117 PCOS and 105 healthy women. The PAI1 insertion/deletion (-675 ins/delG) polymorphism (rs1799768) was genotyped by PCR-SSCP. CYP19A1 [TTTA]n, AR [CAG]n, ESR1 [TA]n, and ESR2 [CA]n genes were evaluated by PCR-based GeneScan analysis, while CYP17A1 5′UTR (rs743572), INSR 1058 CT (rs1799817), and IGF2 3′UTR GA (rs680) polymorphisms were evaluated by PCR-RFLP. The results showed a prevalence of PAI1 4G5G+4G4G genotypes in PCOS (p = 0.025). Younger PCOS women showed a predominance of CT+TT, GA+AA and 4G5G+4G4G genotypes of INSR, IGF2, and PAI1 (p = 0.0499, p = 0.0300, p = 0.0350, respectively). AR shorter alleles (≤ 20 repeats) were significantly associated with higher serum levels of total testosterone (TT, p = 0.0086). In conclusion, PAI1 polymorphism seems to be associated with the risk of PCOS development. Younger PCOS women had specific genotypes of INSR, IGF2 and PAI1 genes. AR shorter alleles can be associated with higher serum levels of TT in PCOS patients.
Modelling the cost effectiveness of rapid point of care diagnostic tests for the control of HIV and other sexually transmitted infections among female sex workers

Background: In sub-Saharan Africa, gonococcal and chlamydial infections are usually managed using the syndromic approach. However, many infections are asymptomatic in women, and the syndromic algorithm has poor sensitivity and specificity for infections caused by Neisseria gonorrhoeae (Ng) and Chlamydia trachomatis (Ct). Because of this, rapid point of care (POC) tests for Ct/Ng could improve sexually transmitted infection (STI) management in women. This study uses mathematical modelling to estimate the incremental cost effectiveness of using POC tests to diagnose Ng/Ct instead of the current syndromic approach used by the SIDA2 HIV/STI prevention project for female sex workers in Cotonou, Benin. Methods: A dynamic mathematical model was used with data from Cotonou to estimate the HIV impact of the existing SIDA2 project (1995–8), and to project how impact would change if POC tests had been used. As observed in test evaluations, the POC tests were assumed to have high specificity, but a range of sensitivities. The incremental economic cost effectiveness of using POC tests was modelled using data on intervention costs and an evaluation of an Ng POC test in Cotonou in 2004. All costs were in 2004 $US. Results: The model estimated the STI treatment aspect of the intervention averted 18 553 Ng/Ct and 359 HIV infections over 4 years when the syndromic approach was used. In contrast, if Ng/Ct had been diagnosed with a 70–80% sensitive and 95% specific POC test then 24–31% fewer clinic attenders would have been treated, 40–60% more Ng/Ct and HIV infections would have been averted, and the incremental cost effectiveness of using them would have been $107–151 per HIV infection averted if the POC tests cost $2 and $58–$81 if they cost $1. Conclusions: POC tests can be a cost effective strategy for substantially increasing the impact on HIV transmission, and decreasing the degree of inappropriate treatment of STI treatment interventions that use syndromic management to diagnose Ng/Ct.