Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection of non-tyramine producing Carnobacterium strains for the biopreservation of cold-smoked salmon

Biogenic amines in fish products are the result of the decarboxylation of free amino-acids by microorganisms. In cold smoked salmon, tyramine is mainly produced by lactic acid bacteria of the genus Carnobacterium that are also interesting bacteria for the control of the risk of Listeria monocytogenes growth. In this study, we have screened a collection of Carnobacterium strains that could be used for biopreservation in order to find a natural tyramine negative strain. This screening was performed using the detection by PCR test of a part of the tyrosine decarboxylase gene. On 35 strains of Carnobacterium tested, all showed the presence of the tdc gene suggesting that they all produce tyramine. This was assessed by the quantification of tyramine production for 10 strains. In a second part, a mutation procedure using ethyl methyl sulfonate was used to select a tyramine negative mutant of Carnobacterium divergens V41,that is a good candidate for biopreservation applications. A mutant strain called C. divergens V41A8 was selected and characterized. The mutant was identical to the wild strain concerning carbohydrates fermentation profile, antibiogram spectrum, bacteriocin production, and bacteriocin spectrum towards Listeria monocytogenes. The growth of strain C. divergens V41A8 was tested by comparison to the wild strain on a sterile cold smoked salmon model. The mutant grew more slowly than the wild strain on the product but it reached nearly the same level after 28 days of storage. Moreover, the production of tyramine detected on cold smoked salmon inoculated with C. divergens V41 (122 µg/g after 28 days of storage) was not detected at all when the product was inoculated with the mutant strain C. divergens V41A8. This strain could be an interesting alternative for the application of biopreservative Carnobacterium on food products naturally contaminated with tyramine such as smoked fishes.
Transition From Gavage to Nipple Feeding for Preterm Infants With Bronchopulmonary Dysplasia

Background:The transition from gavage to nipple feeding is difficult for preterm infants with bronchopulmonary dysplasia because of tachypnea and hypoxemia from chronic respiratory distress. Objective:The aim of this study was to test the hypothesis that preterm infants with bronchopulmonary dysplasia who transitioned from gavage to nipple feeding with the semidemand method would achieve nipple feeding sooner and be discharged from hospital sooner than control infants who received standard care. Methods:Forty-two infants were randomized to the control condition and 44 to the experimental protocol. Mean gestational ages and birth weights were 25 ± 1.5 weeks and 784 g for controls and 25 ± 1.4 weeks and 787 g for experimental infants. Control infants received standard care that included gradual increases in the number of nipple to gavage feedings per day. Experimental infants received the semidemand method that used infant behavioral and cardiorespiratory signs to regulate frequency, length, and volume of nipple feedings. General linear model procedures were used to compare study groups. Results:Experimental infants achieved nipple feeding at M = 5.9 ± 0.7 days compared with control infants, M = 12.3 ± 0.8 (p < .0001). Length of hospitalization was not significantly different between groups. Discussion:The semidemand method significantly shortened the time for infants to attain nipple feeding in a manner taking their respiratory distress into consideration.
A System-On-Chip bus architecture for hardware Trojan protection in security chips

Hardware Trojan, similar to the computer viruses, is a new threat in modern System-On-Chips (SOCs) such as security chips and trusted computer systems. Despite the risks that such an attack entails, little attention has been given to the methods of run-time Trojan detection. In this paper, the defects in existing security chips are analyzed and an improved bus architecture for hardware Trojan protection is presented, which can prevent data from runtime Trojan attacking in the digital circuits. A novel bus controller and random number generator (RNG) are used to implement the mechanism and the experimental results shows that the structure is efficient at thwarting the leaking of confidential information and signals.
Integración desde lo micro: Paradiplomacia y la Comunicación en el Escenario Latinoamericano

Cuantas veces ha visto, en America Latina, a un Gobierno Regional o a un Municipio involucrado en asuntos internacionales, estableciendo canales de comunicacion con otros actores de diferentes partes del globo? A pesar de que todavia no se reconoce como una practica comun, la internacionalizacion de las ciudades es una realidad que lleva ya algunos anos desarrollandose. Considerando este nuevo escenario internacional, cabe preguntar entonces como la diplomacia de los gobiernos subnacionales, denominada paradiplomacia, junto con la comunicacion, fortalece el proceso de integracion regional.
Causal Inference with Intermediates: Simple Methods for Principal Strata Effects and Natural Direct Effects

A central problem in natural science is identifying general laws of cause and effect. Medical science is devoted to revealing causal relationships in humans [1]. The framework for causal inference applied in epidemiology can contribute substantially to clearly specifying and testing causal hypotheses. In some situations, conditioning on an intermediate, which may be between the cause (exposure) and effect (outcome), is of concern for biomedical researchers and public health practitioners [2-4]. In particular, there is a conflict in the perinatal epidemiology literature between the desire to obtain birth-weight-specific associations [5-7] and increasing awareness that conditioning on this variable can give rise to severe biases [8-11]. The difficulty arises because birth weight may be on a pathway from the exposure of interest to the perinatal outcome. For example, if the exposure is maternal smoking and the outcome is infant mortality, maternal smoking may partly affect infant mortality through its effects on fetal growth or on the timing of delivery, thereby potentially through the intermediate, birth weight. In an analysis conditioned on an intermediate, without controlling for the common causes of the intermediate and the outcome, biased results and paradoxical findings can emerge [2-4,12].
Argon metastables in HiPIMS: time-resolved tunable diode-laser diagnostics

Time-resolved tunable diode-laser absorption spectroscopy measurements were performed on the argon metastable (Arm) level 3s23p5 4s excited at 801.478 nm, in the dense plasma region in front of the magnetron target in a high power impulse magnetron sputtering (HiPIMS) discharge. From the Doppler profile the evolution of the temperature and density was derived during the pulse as well as during the plasma decay, i.e. in the afterglow. It is shown that the Arm density sharply increases at the beginning of the discharge pulse, followed by a severe Arm depletion along with increasing gas temperature around the peak of the HiPIMS discharge current. The strong dynamics of these parameters involve many elementary processes such as electron-impact excitation, electron-impact de-excitation and ionization of Arm, gas rarefaction, electron temperature increase at the end of the pulse and gas diffusion. These phenomena are discussed with respect to several parameters: distance from the target, peak discharge current during the pulse, pulse length, and gas pressure.
Establishing Pine Monocultures and Mixed Pine-Hardwood Stands on Reclaimed Surface Mined Land in Eastern Kentucky: Implications for Forest Resilience in a Changing Climate

Surface mining and mine reclamation practices have caused significant forest loss and forest fragmentation in Appalachia. Shortleaf pine (Pinus echinata) is threatened by a variety of stresses, including diseases, pests, poor management, altered fire regimes, and climate change, and the species is the subject of a widescale restoration effort. Surface mines may present opportunity for shortleaf pine restoration; however, the survival and growth of shortleaf pine on these harsh sites has not been critically evaluated. This paper presents first-year survival and growth of native shortleaf pine planted on a reclaimed surface mine, compared to non-native loblolly pine (Pinus taeda), which has been highly successful in previous mined land reclamation plantings. Pine monoculture plots are also compared to pine-hardwood polyculture plots to evaluate effects of planting mix on tree growth and survival, as well as soil health. Initial survival of shortleaf pine is low (42%), but height growth is similar to that of loblolly pine. No differences in survival or growth were observed between monoculture and polyculture treatments. Additional surveys in coming years will address longer-term growth and survival patterns of these species, as well as changes to relevant soil health endpoints, such as soil carbon.
Myc-induced AMPK-phospho p53 pathway activates Bak to sensitize mitochondrial apoptosis

Oncogenic transcription factor Myc deregulates the cell cycle and simultaneously reprograms cellular metabolism to meet the biosynthetic and bioenergetic needs of proliferation. Myc also sensitizes cells to mitochondria-dependent apoptosis. Although metabolic reprogramming has been circumstantially connected to vulnerability to apoptosis, the connecting molecular pathways have remained poorly defined. Here, we show that Myc-induced altered glutamine metabolism involves ATP depletion and activation of the energy sensor AMP-activated protein kinase (AMPK), which induces stabilizing phosphorylation of p53 at Ser15. Under influence of Myc, AMPK-stabilized tumor suppressor protein p53 accumulates in the mitochondria and interacts with the protein complex comprised of B-cell lymphoma 2 (Bcl-2) antagonist/killer (BAK) and Bcl2-like 1 (Bcl-xL). Mitochondrial p53 induces conformational activation of proapoptotic Bak without disrupting the Bak–Bcl-xL interaction. Further liberation of Bak specifically from the p53-activated Bak–Bcl-xL complex leads to spontaneous oligomerization of Bak and apoptosis. Thus, Myc-induced metabolic changes are coupled via AMPK and phospho-p53 to the mitochondrial apoptosis effector Bak, demonstrating a cell-intrinsic mechanism to counteract uncontrolled proliferation.
Utility of postsurgical renal scintigraphy to predict one-year outcome of renal transplants in patients with delayed graft function

ObjectiveDelayed graft function is a frequent complication after kidney transplantation impacting aversely on graft survival. The aim of this study was to assess the prognostic value of quantitative scintigraphic parameters immediately after transplantation in this population. MethodsOne hundred patients with renal transplants suffering from delayed graft function were included in this study. All patients underwent 99mTc-mercaptoacetyltriglycine renal scintigraphy within 72 h of transplantation and were followed for 1 year. Various isotopic parameters were evaluated based on time–activity curves for angiographic and tubular phases. Threshold values for each parameter were derived from receiver operating characteristic curves to study their predictive values for transplant success at 1 year. ResultsMean values of the Kirchner index, tubular function slope, graft/aorta perfusion ratio, or graft uptake/perfusion ratio were significantly higher in successfully grafted patients (P<0.05). The Kirchner index yielded the largest area under the receiver operating characteristic curves (0.75). The tubular function slope (odds ratio>1.4) was found to be an independent prognostic factor for 1-year renal graft failure. ConclusionOur study confirms the prognostic value of vascular parameters in renal transplants, especially the Kirchner index whose negative predictive value was more than 90% for kidney transplantation 1-year success. In addition, isotopic parameters assessing the nephronic functional mass or the functional renal reserve seemed to be relevant prognostic tools with respect to 1-year outcomes. Therefore, the assessment of vascularization and renal function using an early 99mTc-mercaptoacetyltriglycine renal scintigraphy seems to be a powerful tool in establishing 1-year prognosis of renal allografts.
Formation of Secondary Containment Systems Using Permeation of Colloidal Silica

U.S. Environmental Protection Agency (USEPA) regulations require the capture of spills from liquid tanks containing hazardous chemicals by using a secondary containment system. Compacted clay or geomembrane liners are commonly used in secondary containment systems, but they are cumbersome when used in conjunction with existing liquid tanks because of pipeline networks surrounding the tanks. This study evaluates the formation of hydraulic barriers for secondary containment through the permeation of colloidal silica grout. A sim- plified infiltration model is presented to predict the downward movement of the colloidal silica grout into a soil layer, considering the time- dependent increase in dynamic viscosity of the colloidal silica for different concentrations of an electrolyte accelerator. Because the simplified infiltration model cannot predict the soil-grout interaction or the permeation of the colloidal silica by fingering, its results were calibrated by using the observations from a large-scale column test involving the permeation of colloidal silica into sand. The predicted position of the wetting front was found to match that of the experiment when the parameter governing the change in viscosity of the colloidal silica was increased by a factor of 30. The infiltration model calibrated with observations from column infiltration experiments provides a simple approach to the design of the secondary containment systems using permeation of colloidal silica. DOI: 10.1061/(ASCE)EE.1943- 7870.0000345. © 2011 American Society of Civil Engineers.
A mitogenic view on the evolutionary history of the Holarctic freshwater gadoid, burbot (Lota lota)

Climatic oscillations during the Pleistocene epoch had a dramatic impact on the distribution of biota in the northern hemisphere. In order to trace glacial refugia and postglacial colonization routes on a global scale, we studied mitochondrial DNA sequence variation in a freshwater fish (burbot, Lota lota; Teleostei, Gadidae) with a circumpolar distribution. The subdivision of burbot in the subspecies Lota lota lota (Eurasia and Alaska) and Lota lota maculosa (North America, south of the Great Slave Lake) was reflected in two distinct mitochondrial lineages (average genetic distance is 2.08%). The lota form was characterized by 30 closely related haplotypes and a large part of its range (from Central Europe to Beringia) was characterized by two widespread ancestral haplotypes, implying that transcontinental exchange/migration was possible for cold‐adapted freshwater taxa in recent evolutionary time. However, the derived mitochondrial variants observed in peripheral populations point to a recent separation from the core group and postglacial recolonization from distinct refugia. Beringia served as refuge from where L. l. lota dispersed southward into North America after the last glacial maximum. Genetic variation in the maculosa form consisted of three mitochondrial clades, which were linked to at least three southern refugia in North America. Two mitochondrial clades east of the Continental Divide (Mississippian and Missourian clades) had a distinct geographical distribution in the southern refuge zones but intergraded in the previously glaciated area. The third clade (Pacific) was exclusively found west of the Continental Divide.
Florida Panther Habitat Selection Analysis of Concurrent GPS and VHF Telemetry Data

Abstract Florida panthers (Puma concolor coryi) are listed as an endangered subspecies in the United States and they exist in a single Florida population with <100 individuals; all known reproduction occurs south of Lake Okeechobee. Habitat loss is the biggest threat to this small population and previous studies of habitat selection have relied on very high frequency (VHF) telemetry data collected almost exclusively during diurnal periods. We investigated habitat selection of 12 panthers in the northern portion of the breeding range using 1) Global Positioning System (GPS) telemetry data collected during nocturnal and diurnal periods and 2) VHF telemetry data collected only during diurnal periods. Analysis of both types of telemetry data yielded similar results as panthers selected upland (P < 0.001) and wetland (P < 0.001) forested habitat types. Our results indicated that forests are the habitats selected by panthers and generally support the current United States Fish and Wildlife Service panther habitat ranking system. We suggest that future studies with greater numbers of panthers should investigate panther habitat selection using GPS telemetry data collected throughout the range of the Florida panther and with location attempts scheduled more evenly across the diel period. Global Positioning System radiocollars were effective at obtaining previously unavailable nocturnal telemetry data on panthers; however, we recommend that panther researchers continue to collect VHF telemetry data until acquisition rates and durability of GPS collars improve.
Pathogenesis of psoriatic arthritis

Purpose of reviewHeterogeneity in clinical presentation and disease course has hindered understanding of disease mechanisms in psoriatic arthritis, but recent studies have provided insights into pathogenesis. This review examines relevant animal models and genetic factors implicated in disease susceptibility. Also, recent reports on mechanisms related to synovial and entheseal inflammation are discussed. Recent findingsTwo transgenic mouse models (amphiregulin, STAT-3) were reported that have features of psoriatic arthritis and psoriasis respectively. Genetic studies did not find associations between psoriatic arthritis and several class I major histocompatibility complex alleles, the caspase-activating recruitment domain 15 domain, or the major histocompatibility complex class I chain-related gene A9 allele, in sharp contrast to previous reports. The striking association of psoriatic arthritis with mutations in the killer immunoglobulin receptors on natural killer cells is particularly exciting but needs further study. Psoriatic arthritis has histopathologic features that are more characteristic of other forms of spondyloarthritis than rheumatoid arthritis. Moreover, several of these features correlate with clinical disease activity. Matrix metalloproteinases are strongly expressed in psoriatic arthritis synovium, and serum matrix metalloproteinases-3 may be a reliable biomarker for monitoring disease response. Finally, the concept of an ‘enthesis organ’ may explain the magnetic resonance imaging findings and clinical signs of psoriatic enthesitis and dactylitis. SummaryRecent findings highlight the importance of innate immune mechanisms in disease pathogenesis. Moreover, psoriatic arthritis and rheumatoid arthritis synovium have divergent histopathologic features that indicate distinct disease mechanisms. The generation of appropriate animal models coupled with reliable biomarkers will result in a deeper understanding of disease pathogenesis and will facilitate the identification of new therapeutic targets.
Using of Hibiscus Sabdariffa extract as a natural histological stain of the Skin

Objective: this experimental comparative study aimed to explore the efficiency of Hibiscus Sabdariffa as natural staining dye for skin tissue histological sections as compared to the routinely and commonly used stain, hematoxylin and eosin. Methods: paraffin-embedded formalin-fixed tissue sections from skin were stained by different concentrations of Hibiscus Sabdariffa solution in different times at room temperature and compared to H&E-stained sections. Results: the best results were obtained when 5% solution was used. The best time duration for staining was 60 minutes. Conclusions: Hibiscus Sabdariffa solution can be used as a cytoplasmic stain instead of eosin in the H&E method to stain formalin-fixed paraffin-embedded skin tissue sections.
Infection after depressed fracture of skull. Implications for management of nonmissile injuries.

✓ The authors analyze and discuss the 10% infection rate among 359 civilians with compound skull fractures. Infection results from incomplete debridement, for which antibiotics are no substitute. Inadequate treatment usually derives from missing the diagnosis of depressed fracture completely, but sometimes from underestimating the seriousness of the individual injury. Many patients with this injury never lose consciousness, do not have immediate x-ray studies, and are not admitted to hospital; infection is a serious risk in this group. Complete removal of all bone fragments, as recommended for missile injuries, is not necessary. If bone is replaced, the incidence of infection (and of epilepsy) is not greater, and the need for cranioplasty avoided; bone can be safely replaced even when surgery is delayed for 24 hours and when the dura is torn.
An Adaptive Redundancy Scheme for TCP with Network Coding

To address the inability of the standard TCP protocol to distinguish between congestive losses and random packet losses produced by the noisy channel, in this paper we propose an adaptive algorithm to dynamically adjust the redundancy factor $R$ of the TPC/NC protocol proposed by Sundararajan et al. by adding some additional functionalities to the original network coding layer. We define a loss differentiation scheme to adjust $R$, based on the Vegas Loss Predictor and the collective feedback information of ACKs and duplicates ACKs, which are both indicators of the network condition. In that way the source adjusts intelligently $R$ based on the network conditions, avoiding unnecessary TCP rate reduction due to packet losses induced by the noisy channel and preventing the network from entering in a congestion state. Our TPC/NC implementation with our adaptive scheme is full-duplex, and can manage multiple TCP connections simultaneously. Simulation results over realistic network scenarios using OPNET Modeler show that our adaptive scheme in conjunction with the standard TCP/NC produces better TCP-throughputs than the standard TCP/NC, TCP-Reno, TPC New Reno, and TCP Reno with SACKS.
Plasticity of the nigropallidal pathway in Parkinson's disease

The degeneration of nigrostriatal dopamine neurons in early Parkinson's disease (PD) is compensated in part by increased transmitter turnover in surviving neurons of the pathway. In this 18F‐dopa positron emission tomography study, we demonstrate compensatory changes in PD in another midbrain dopamine projection to the basal ganglia, the nigropallidal projection to the internal segment of the globus pallidus (GPi). Increased 18F‐dopa uptake in the GPi is seen in early PD which then is lost in advanced PD. Our early PD cases show an absence of significant clinical progression in the face of a continuing loss of nigrostriatal projections. This indicates a compensatory neuronal plasticity that we now show to involve the nigropallidal dopamine pathway to the GPi but not to the external segment of the globus pallidus (GPe). Enhanced function of the dopamine projection to the GPi serves, we propose, to maintain a more normal pattern of pallidal output to ventral thalamus and motor cortex in early PD, whereas loss of this adaptive pathway in advanced disease may be a pivotal step in the progression of the disease.