Miracle-dz/UniFAR-FTUs huggingface dataset:
Self‐assembly and recrystallization of bacterial S‐layer proteins at silicon supports imaged in real time by atomic force microscopy

The self‐assembly of bacterial surface‐layer (S‐layer) proteins (SbpA of Bacillus sphaericus CCM 2177) at silicon supports (hydrophobic, non‐plasma‐treated and hydrophilic, O2 plasma‐treated silicon supports) was imaged in real time by atomic force microscopy (AFM). A closed mosaic layer consisting of small crystals (less than 200 nm in diameter) was formed at a hydrophobic silicon support, whereas a coherent crystalline lattice consisting of large domains (2–10 µm in size) was generated at O2 plasma‐treated, hydrophilic silicon wafers. The structure of the formed layers was a monolayer (9 nm in height) at the hydrophobic silicon and a bilayer (15 nm in height) at the hydrophilic silicon. In situ AFM measurements confirmed the importance of ionic bonds in the formation of crystalline SbpA layers at silicon supports. Rupture of the protein subunits with a metal chelator from the crystalline lattice of SbpA was visualized in situ by AFM. The stability of solid‐supported SbpA layers could be enhanced by cross‐linking the S‐layers with amino–amino or amino–carboxyl group directed cross‐linkers.
Potentiation of inhibitory glycinergic neurotransmission by Zn2+: a synergistic interplay between presynaptic P2X2 and postsynaptic glycine receptors

The divalent cation zinc is known to modulate chloride currents carried by native and recombinant mammalian glycine receptors (GlyRs). To unravel the effect of Zn2+ on glycinergic neurotransmission, inhibitory postsynaptic currents (IPSC) of rat spinal neurons grown in culture were analysed in the absence and presence of Zn2+. Low concentrations of Zn2+ (0.5 and 5 µm) augmented the mean amplitude of miniature IPSCs by ≈ 40% over values obtained in the absence of zinc, whereas higher concentrations of Zn2+ (50 µm) significantly decreased mean amplitude values. Remarkably, low concentrations of Zn2+ also significantly increased the mean frequency of miniature IPSCs. This effect was blocked by the P2X receptor antagonists PPADS and suramin, indicating the presence of Zn2+‐sensitive presynaptic P2X receptors on glycinergic terminals. Immunostaining with antibodies against different P2X receptor subtypes revealed that P2X2 receptors partially colocalize with the GlyR. Potentiating concentrations of Zn2+ also affected the kinetics of miniature and evoked IPSCs by significantly prolonging their decay time constants. Electrophysiological analysis of heterologously expressed glycine transporters (GlyT) revealed for GlyT2 zero, and for GlyT1 a modest (< 20%), reduction of glycine uptake in the presence of 5 µm Zn2+, indicating that prolongation of glycinergic IPSCs by Zn2+ is not due to inhibition of glycine removal from the synaptic cleft. Together, these results suggest that Zn2+ is a potent modulator of glycinergic synaptic transmission which increases in a synergistic manner the agonist affinity of both presynaptic P2X2 receptors and postsynaptic GlyRs.
Systemic redox modifications in senile cataract.

UNLABELLED Recent studies on cataract formation focus on a primary role of systemic oxidative stress, generated outside the lens. Plasma inflammatory markers are associated with senile cataract. OBJECTIVE The aim of this study was to find correlations between blood oxidative stress markers and some inflammatory plasma markers in cataractous patients. DESIGN AND METHODS The blood samples were collected from 38 patients (aged 50 to 80). Patients were subdivided according to two criteria. Considering age criteria, presenile and senile cataract groups were formed. According to the absence or presence of other ocular comorbidities (age-related macular degeneration, glaucoma), pure cataract and nonpure cataract groups were constituted. Fifteen age and sex matched healthy subjects were selected for the control group. RESULTS In our study, for all groups of patients, the measured markers of oxidative stress were modified vs. control values. Plasma antioxidant capacity, plasma antioxidant "gap", cholesterol and albumin/globulin levels were significantly decreased while RBC SOD activity, RBC catalase activity and plasma ceruloplasmin were significantly increased. Inflammatory markers, ceruloplasmin and albumin/globulins were correlated with different parameters of oxidative stress. CONCLUSION The blood redox values and the level of some inflammatory markers demonstrate that senile cataract is a systemic disease with an inflammatory component.
Cognitive impairment, clinical course and treatment history in out-patients with bipolar affective disorder: relationship to tardive dyskinesia

SYNOPSIS Clinical, neuropsychological and psychopharmacological characteristics were investigated for their ability to distinguish individuals with and without involuntary movements (tardive dyskinesia), among a population of 40 out-patients with bipolar affective disorder and a history of exposure to neuroleptics and lithium. Impaired performance on a test of cognitive flexibility bore the primary association with both the presence and the severity of involuntary movements. The additional relationships identified emphasized further that individual vulnerability to involuntary movements appeared to be associated not with greater duration or dosage of treatment, but with features of the bipolar illness, including number and type of affective episodes, for which that treatment was prescribed.
Optimized Precision - A New Measure for Classifier Performance Evaluation

All learning algorithms attempt to improve the accuracy of a classification system. However, the effectiveness of such a system is dependent on the heuristic used by the learning paradigm to measure performance. This paper demonstrates that the use of Precision (P) for performance evaluation of imbalanced data sets could lead the solution towards sub-optimal answers. We move onto present a novel performance heuristic, the 'Optimized Precision (OP)', to negate these detrimental effects. We also analyze the impact of these observations on the training performance of ensemble learners and Multi-Classifier Systems (MCS), and provide guidelines for the proper training of multi-classifier systems.
U.S. Demand for Fresh Fruit Imports

Over the last three decades, U.S. imports of fresh fruits have been constantly increasing at an annual average growth rate of 7% (USITC, 2016). Fresh fruits make up 9% of the total U.S. food imports (UN Database, 2016) with the top seven fruits accounting for 82% of the value of the U.S. fresh fruit imports and Canada and Mexico (NAFTA countries) as the most important trade partners (USITC, 2016). This study analyzes the main U.S. markets and supply sources of the top imported fresh fruits and estimates a Source-Differentiated Almost Ideal Demand System model (SDAIDS) using time-series data, with North American Free Trade Agreement (NAFTA) countries and the rest of the world (ROW) as import sources. Our results suggest that source of origin is an intrinsic quality attribute for most of the fresh fruits analyzed. More specifically, the study found that most uncompensated own-price elasticities are inelastic, most cross-price elasticities are positives indicating that the fruits imported from given sources are net substitutes, and that statistically significant expenditure elasticities are positive implying that the quantity imported of all the fresh fruit analyzed increases as real expenditure for those fruits rises. The results of this study will be useful to policy-makers in regulating the international market of fresh fruits, setting optimal import taxes and price floors, and predicting likely scenarios of imports from Canada and Mexico.
Structural and Functional Differences in Two Cyclic Bacteriocins with the Same Sequences Produced by Lactobacilli

ABSTRACT Lactobacillus gasseri LA39 and L. reuteri LA6 isolated from feces of the same human infant were found to produce similar cyclic bacteriocins (named gassericin A and reutericin 6, respectively) that cannot be distinguished by molecular weights or primary amino acid sequences. However, reutericin 6 has a narrower spectrum than gassericin A. In this study, gassericin A inhibited the growth of L. reuteri LA6, but reutericin 6 did not inhibit the growth of L. gasseri LA39. Both bacteriocins caused potassium ion efflux from indicator cells and liposomes, but the amounts of efflux and patterns of action were different. Although circular dichroism spectra of purified bacteriocins revealed that both antibacterial peptides are composed mainly of α-helices, the spectra of the bacteriocins did not coincide. The results of d- and l-amino acid composition analysis showed that two residues and one residue of d-Ala were detected among 18 Ala residues of gassericin A and reutericin 6, respectively. These findings suggest that the different d-alanine contents of the bacteriocins may cause the differences in modes of action, amounts of potassium ion efflux, and secondary structures. This is the first report that characteristics of native bacteriocins produced by wild lactobacillus strains having the same structural genes are influenced by a difference in d-amino acid contents in the molecules.
Use of LDL receptor—targeting peptide vectors for in vitro and in vivo cargo transport across the blood‐brain barrier

The blood‐brain barrier (BBB) prevents the entry of many drugs into the brain and, thus, is a major obstacle in the treatment of CNS diseases. There is some evidence that the LDL receptor (LDLR) is expressed at the BBB and may participate in the transport of endogenous ligands from blood to brain, a process referred to as receptor‐mediated transcytosis. We previously described a family of peptide vectors that were developed to target the LDLR. In the present study, in vitro BBB models that were derived from wild‐type and LDLR‐knockout animals (ldlr‒/‒) were used to validate the specific LDLR‐dependent transcytosis of LDL via a nondegradative route. We next showed that LDLR‐targeting peptide vectors, whether in fusion or chemically conjugated to an Ab Fc fragment, promote binding to apical LDLR and transendothelial transfer of the Fc fragment across BBB monolayers via the same route as LDL. Finally, we demonstrated in vivo that LDLR significantly contributes to the brain uptake of vectorized Fc. We thus provide further evidence that LDLR is a relevant receptor for CNS drug delivery via receptor‐mediated transcytosis and that the peptide vectors we developed have the potential to transport drugs, including proteins or Ab based, across the BBB. —Molino, Y. , David, M. , Varini, K. , Jabès, F. , Gaudin, N. , Fortoul, A. , Bakloul, K. , Masse, M. , Bernard, A. , Drobecq, L. , Lécorché, P., Temsamani, J., Jacquot, G. , Khrestchatisky, M. Use of LDL receptor–targeting peptide vectors for in vitro and in vivo cargo transport across the blood‐brain barrier. FASEB J. 31, 1807–1827 (2017). www.fasebj. org
Transvaginal Ultrasonography of the Cervix to Predict Preterm Birth in Women With Uterine Anomalies

Objective: Women with uterine anomalies have higher rates of preterm birth, but the reason for this has not been elucidated. Transvaginal ultrasound examination has been shown to be an accurate test for the prediction of preterm birth but has not been studied specifically in this population. Methods: Pregnant women with uterine anomalies were followed prospectively with transvaginal ultrasound examination of the cervix, performed between 14 and 23 6/7 weeks of gestation. A short cervical length was defined as less than 25 mm of cervical length. The primary outcome was spontaneous preterm birth, defined as birth at less than 35 weeks. Results: Of the 64 pregnancies available for analysis, there were 28 with a bicornuate uterus, 13 with a septate uterus, 11 with a uterine didelphys, and 12 with a unicornuate uterus. The overall incidence of spontaneous preterm birth at less than 35 weeks was 11%. Of the 10 (16%) women with a short cervical length, 5 (50%) had spontaneous preterm birth. Of the 54 women without a short cervical length, only 2 (4%) had a spontaneous preterm birth. The sensitivity, specificity, and positive and negative predictive values of a short cervical length for spontaneous preterm birth were 71%, 91%, 50%, and 96%, respectively (relative risk 13.5, 95% confidence interval 3.49–54.74). Of the 7 women with both short cervical length and preterm birth, all uterine subtypes were represented except septate uterus. Conclusion: A short cervical length on transvaginal ultrasonography in women with uterine anomalies has a 13-fold risk for preterm birth. Unicornuate uterus had the highest rate of cervical shortening and preterm delivery. Level of Evidence: II-2
FlashBench: A workbench for a rapid development of flash-based storage devices

As the cell size of NAND flash memory is shrinking, its physical characteristics such as performance and lifetime are significantly degraded. As effective solutions of overcoming such poor physical characteristics, more cross-layer system-level approaches (such as compression and deduplication techniques) are expected to be developed. These system-level techniques typically employ intelligent software algorithms supported by specialized hardware accelerators. Using hardware accelerators combined with sophisticated software algorithms greatly increases the design complexity of flash-based storage devices. However, existing storage design environments are not adequate enough to handle this increased design complexity in a timely and efficient manner. To address this new challenge, we propose a novel storage development environment, called FlashBench, that helps developers to build high-complexity storage solutions quickly. FlashBench is designed to provide a generic framework for the rapid development and validation of storage software/hardware algorithms by supporting multi-level design environments, specifically optimized for seamless hardware/software cross-layer integrations. Our case study demonstrates that FlashBench enables developers to implement high-complexity flash devices with specialized optimization functions in a shorter development time over traditional design environments.
Maternal plasma corticotropin-releasing hormone trajectories vary depending on the cause of preterm delivery.

OBJECTIVE Although second trimester maternal plasma corticotropin-releasing hormone concentrations are elevated in women who are destined to deliver preterm, the sensitivity and positive predictive value of an individual test of corticotropin-releasing hormone concentration is low. This poor screening performance may be due in part to the observation that the causes of preterm delivery are heterogenous, with potentially different effects on corticotropin-releasing hormone production. We have reanalyzed data from a previous cohort of women with multiple samplings to determine whether the trajectory of increase of placental corticotropin-releasing hormone provided more information than did a single sample. STUDY DESIGN In this cohort, where 2 to 4 samples that had been assayed for corticotropin-releasing hormone were available on 305 women, the general form of the exponential equation y = ae(bt) was fitted to the corticotropin-releasing hormone data of each individual by the Gauss-Newton nonlinear least squares method, which generated the parameters, y-intercept and rate of rise, in corticotropin-releasing hormone concentration for each woman. Nonparametric statistical techniques, including bootstrapping, were applied to compare the results for the group of women who delivered at term with the group of women who delivered spontaneously preterm and the group of women who were delivered preterm by induction or cesarean delivery because of obstetric indication. RESULTS The 3 clinically defined groups have significantly different parameters, y-intercept and rate of rise, which describe the corticotropin-releasing hormone trajectory. The group that delivered preterm because of obstetric indications had a similar mean y-intercept but significantly greater mean rate of rise in corticotropin-releasing hormone concentration than the term group (0.3491 vs 0.1788; 95% CI, 0.2331-0.4615 vs 0.1394-0.2330). The group that delivered spontaneously preterm had a significantly greater mean y-intercept than the group that delivered preterm because of obstetric indication (17.08 vs 1.83; 95% CI, 5.89-28.43 vs 0.03-5.19) but a similar mean rate of rise to the group that delivered at term. CONCLUSION These data suggest that spontaneous preterm delivery is associated with an abnormal setting of the production of corticotropin-releasing hormone that is present from very early in pregnancy, although women who experience an induced preterm delivery are characterized by rapidly rising placental corticotropin-releasing hormone concentrations. These data further suggest that clinical abnormalities that are associated with preterm delivery by induction or cesarean delivery are associated with abnormalities that lead to a rapidly increasing corticotropin-releasing hormone concentrations. Trajectories for corticotropin-releasing hormone provide information beyond that obtained from a single sample.
Repeat Gamma Knife surgery for vestibular schwannomas

Background: Gamma Knife (GK) surgery is a recognized treatment option for the management of small to medium-sized vestibular schwannoma (VS) associated with high-tumor control and low morbidity. When a radiosurgical treatment fails to stop tumor growth, repeat GK surgery can be proposed in selected cases. Methods: A series of 27 GK retreatments was performed in 25 patients with VS; 2 patients underwent three procedures. The median time interval between GK treatments was 45 months. The median margin dose used for the first, second, and third GK treatments was 12 Gy, 12 Gy, and 14 Gy, respectively. Six patients (4 patients for the second irradiation and 2 patients for the third irradiation) with partial tumor regrowth were treated only on the growing part of the tumor using a median margin dose of 13 Gy. The median tumor volume was 0.9, 2.3, and 0.7 cc for the first, second, and third treatments, respectively. Stereotactic positron emission tomography (PET) guidance was used for dose planning in 6 cases. Results: Mean follow-up duration was 46 months (range 24–110). At the last follow-up, 85% of schwannomas were controlled. The tumor volume decreased, remained unchanged, or increased after retreatment in 15, 8, and 4 cases, respectively. Four patients had PET during follow-up, and all showed a significant metabolic decrease of the tumor. Hearing was not preserved after retreatment in any patients. New facial or trigeminal palsy did not occur after retreatment. Conclusions: Our results support the long-term efficacy and low morbidity of repeat GK treatment for selected patients with tumor growth after initial treatment.
Prognostic significance of lymph node ratio after resection of peri-hilar cholangiocarcinoma.

BACKGROUND Lymph node (LN) metastases are a major negative prognostic factor for peri-hilar cholangiocarcinoma (PCC). Prognostic significance of the extent of LN dissection, number of metastatic LN and the lymph node ratio (LNR) are still under debate. AIMS The aims of the present study were to evaluate the prognostic value of the LN status, the total number of LNs evaluated and LNR in PCC. METHODS Between 1990 and 2008, 62 patients with PCC submitted to surgical resection with curative intent were retrospectively evaluated. Number and status of harvested LN were recorded. RESULTS In 53 patients (85.4%) regional lymphadenectomy was performed. Median number of LNs examined was 7 (range 1-25). Median survival was 41.9 months in patients with N0 compared with 22.7 months in 21 patients (39.6%) with N+ (P= 0.03). Median survival was 3, 18.5 and 29 months for patients with 0, 1-3 and >3 LN retrieved, respectively (P < 0.01). Five-year survival for patients above and below the LNR cut-off value of 0.25 was 0% and 22.5%, respectively (P= 0.03). CONCLUSIONS LN metastases are a major prognostic factor for survival after surgical resection of PCC. The number of LN harvested and LNR showed high prognostic value.
Examining Effects of School and Teacher Inputs on Productive Efficiency of Ugandan Primary Schools: A Stochastic Frontier Analysis

This study evaluates the extent to which school and teacher quality inputs affect technical efficiency of primary schools in Uganda. Using stochastic frontier analysis, the study found textbook-pupil ratio, classroom-pupil ratio and teacher-pupil ratio exhibit increasing returns to scale on literacy and numeracy scores, and school mean efficiency varied widely across the four districts. Moreover, per pupil family expense on education, parent education and teacher salary demonstrate significant positive effect on pupil academic achievement while high rate of teacher absenteeism is detrimental to pupil performance. The study concludes that provision of basic requirements is not sufficient for pupil achievement and school productivity, but rather improving institutional organization to mobilize centres of power and capacity to use available scarce resources for productive gains should be promoted.
Resolving ethical challenges when researching with minority and vulnerable populations: LGBTIQ victims of violence, harassment and bullying

This article provides an analysis of the issues and ethical challenges faced in a study with LGBTIQ student participants concerning their experiences of violence, harassment and bullying in tertiary settings. The authors detail the ethical challenges behind the development of the project, and around conducting research with a minority and vulnerable population. The article illustrates how the utilization of feminist and queer theory has impacted the process of conducting ethical research, including approaches to recruitment and participant autonomy. The dilemmas of confidentiality within a self-labelled and easily identifiable population are resolved. Further, unexpected challenges and risks to participant safety created through adherence to institutional ethical research frameworks are rectified. Importantly, the authors seek to avoid revictimization of participants and to instead empower students in their responses to violence, harassment and bullying that they may have experienced. The authors point to utilization of theoretical foundations and continual reflexive improvement as elements of best practice for those seeking to research minority populations, and in projects marked by the participation of those deemed vulnerable and high-risk.