Miracle-dz/UniFAR-FTUs huggingface dataset:
Residual eDNA detection sensitivity assessed by quantitative real‐time PCR in a river ecosystem

Several studies have demonstrated that environmental DNA (eDNA) can be used to detect the presence of aquatic species, days to weeks after the target species has been removed. However, most studies used eDNA analysis in lentic systems (ponds or lakes), or in controlled laboratory experiments. While eDNA degrades rapidly in all aquatic systems, it also undergoes dilution effects and physical destruction in flowing systems, complicating detection in rivers. However, some eDNA (i.e. residual eDNA) can be retained in aquatic systems, even those subject to high flow regimes. Our goal was to determine residual eDNA detection sensitivity using quantitative real‐time polymerase chain reaction (qRT–PCR), in a flowing, uncontrolled river after the eDNA source was removed from the system; we repeated the experiment over 2 years. Residual eDNA had the strongest signal strength at the original source site and was detectable there up to 11.5 h after eDNA source removal. Residual eDNA signal strength decreased as sampling distance downstream from the eDNA source site increased, and was no longer detectable at the source site 48 h after the eDNA source water was exhausted in both experiments. This experiment shows that residual eDNA sampled in surface water can be mapped quantitatively using qRT–PCR, which allows a more accurate spatial identification of the target species location in lotic systems, and relative residual eDNA signal strength may allow the determination of the timing of the presence of target species.
Possibilities of carbon black recovery from waste tyre pyrolysis to be used as additive in rubber goods -a review-

This work deals with the literature review of the main carbon black (CB) properties required for reinforcing-filler rubber applications. Commercial CB is rich-carbon material widely used as reinforcing filler in rubber goods. When waste tyres are transformed by pyrolysis, the obtained solid fraction known as pyrolytic carbon black (CBp) contains the original CB (80-90 wt.%) added in tyre manufacturing process along with sulphur (1-3 wt.%) and a representative quantity of inorganics (10-15 wt.%). Taking this into account, it could be inferred that some physical-chemical properties of CBp are similar to those of the original CB. This fact has encouraged the use of CBp as an alternative substitute of CB in different rubber applications. However, it has been found that CBp can be used in certain rubber applications, some research works have also noted the detrimental of some mechanical properties. The inorganics presence in CBp limits some important properties such as tensile strength, tear strength, and hardness in the rubber composites. Also, these compounds as well as some carbonaceous deposits seem to affect the surface area and the surface chemistry, and therefore the active sites, affecting the reinforcing activity. To overcome these limitations, some post-treatments processes are proposed.
Parallel Decoders of Polar Codes

In this letter, we propose parallel SC (Successive Cancellation) decoder and parallel SC-List decoder for polar codes. The parallel decoder is composed of M=2^m(m>=1) component decoders working in parallel and each component decoder decodes a Polar code of a block size of 1/M of the original Polar code. Therefore the parallel decoder has M times faster decoding speed. Our simulation results show that the parallel decoder has almost the same error-rate performance as the conventional non-parallel decoder.
Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients

A Well-Defined Path Although chemokines have long been thought to direct immune cell movements within tissues, a formal in vivo demonstration and detailed understanding are lacking. By tracking dendritic cell movements in the ears of mice, Weber et al. (p. 328) were able to provide both. Endogenous gradients of the chemokine CCL21 were observed in ear tissue and, at distances of up 90 µm, dendritic cells were able to use these gradients to migrate directionally toward lymphatic vessels. The CCL21 gradient was immobilized on heparan sulfates and disruption of the gradient inhibited dendritic cell migration. In mouse skin, immune cells migrate toward lymphatic vessels along an immobilized chemokine gradient. Directional guidance of cells via gradients of chemokines is considered crucial for embryonic development, cancer dissemination, and immune responses. Nevertheless, the concept still lacks direct experimental confirmation in vivo. Here, we identify endogenous gradients of the chemokine CCL21 within mouse skin and show that they guide dendritic cells toward lymphatic vessels. Quantitative imaging reveals depots of CCL21 within lymphatic endothelial cells and steeply decaying gradients within the perilymphatic interstitium. These gradients match the migratory patterns of the dendritic cells, which directionally approach vessels from a distance of up to 90-micrometers. Interstitial CCL21 is immobilized to heparan sulfates, and its experimental delocalization or swamping the endogenous gradients abolishes directed migration. These findings functionally establish the concept of haptotaxis, directed migration along immobilized gradients, in tissues.
Cisplatin Chemoradiotherapy vs Radiotherapy in FIGO Stage IIIB Squamous Cell Carcinoma of the Uterine Cervix: A Randomized Clinical Trial

Importance The evidence for concurrent chemoradiotherapy (CT-RT) in International Federation of Gynecology and Obstetrics (FIGO) stage IIIB squamous cell carcinoma of the uterine cervix is not robust. This study reports the final results of a randomized clinical trial of concurrent cisplatin-based CT-RT and radiotherapy alone (RT) in women with FIGO stage IIIB squamous cell carcinoma of the uterine cervix. Objective To investigate the benefit of concurrent CT-RT in FIGO stage IIIB squamous cell carcinoma of the uterine cervix. Design, Setting, and Participants This phase 3 open-label randomized clinical trial accrued 850 women in Mumbai, India, between July 7, 2003, and September 22, 2011. Of 2121 screened, 850 women with FIGO stage IIIB squamous cell carcinoma of the uterine cervix suitable for concurrent cisplatin chemotherapy were randomly assigned to CT-RT and RT using block randomization (1:1). The data were updated for a minimum follow-up period of 5 years until December 2016. The final analyses were performed in February and March 2017. This single-institution study was conducted at a tertiary cancer center setting. Interventions Randomization to receive RT (RT arm), comprising a combination of external beam RT (50 Gy in 25 fractions over 5 weeks) and brachytherapy, or to receive in addition to the same RT concurrent weekly cisplatin chemotherapy (40 mg/m2 per week) (CT-RT arm). Main Outcomes and Measures The primary end point was 5-year disease-free survival (DFS), defined as the time between the date of randomization and the date of any recurrence or death (whichever occurred first) in the intent-to-treat population. Results This trial included 424 women assigned to CT-RT (mean [SD] age, 49.4 [7.9] years) and 426 women assigned to RT (mean [SD] age, 49.3 [7.9] years). At a median follow-up of 88 months (interquartile range, 61.3-113.1 months), there were 222 recurrences and 213 deaths in the CT-RT arm and 252 recurrences and 243 deaths in the RT arm. The 5-year DFS was significantly higher in the CT-RT arm (52.3%; 95% CI, 52.2%-52.4%) compared with the RT arm (43.8%; 95% CI, 43.7%-43.9%), with a hazard ratio for relapse or death of 0.81 (95% CI, 0.68-0.98) (P = .03). Similarly, the 5-year overall survival (OS) was significantly higher in the CT-RT arm (54.0%; 95% CI, 53.9%-54.1%) compared with the RT arm (46.0%; 95% CI, 45.9%-46.1%), with a hazard ratio for death of 0.82 (95% CI, 0.68-0.98; P = .04). After adjusting for prognostic factors, CT-RT continued to be significantly superior to RT for DFS and OS. There was a higher incidence of acute hematological adverse effects in the CT-RT arm. Conclusions and Relevance Chemoradiotherapy using weekly cisplatin results in significantly better DFS and OS compared with RT in women with stage IIIB squamous cell carcinoma of the uterine cervix. This study provides level 1 evidence in the largest clinical trial reported so far in favor of concurrent weekly cisplatin chemotherapy in this setting. Trial Registration clinicaltrials.gov Identifier: NCT00193791
Clinical and molecular aspects of lead toxicity: An update

Abstract Lead toxicity is a major public health issue in developed and developing countries. Both acute and chronic lead exposure has the potential to cause many deleterious systematic effects including hypertension, frank anemia, cognitive deficits, infertility, immune imbalances, delayed skeletal and deciduous dental development, vitamin D deficiency, and gastrointestinal effects. The underlying mechanisms for all these systemic effects have not been elucidated completely. However, the most plausible cause is free radical damage. In addition to this, lead being a divalent cation can surrogate for calcium at multiple levels affecting various cell signaling pathways. The molecular basis of lead exposure resulting in various systemic effects is being extensively explored. The reports include single nucleotide polymorphisms, epigenetic modifications in susceptible individuals, and the most recent reports also feature regulatory RNA molecules – miRNAs. However, many genetic targets are identified, but their possible mechanisms are still an area to be explored. Additional studies are needed in different population groups to validate the existing findings, as well as to find newer targets that may help in better understanding the molecular mechanisms contributing to lead toxicity. Furthermore, newer strategies for lead risk assessment becomes necessary as the previously recognized “safe” level of lead is also being found to be associated with negative health outcomes.
Paresthesias Among Community Members Exposed to the World Trade Center Disaster

Objective: Paresthesias can result from metabolic disorders, nerve entrapment following repetitive motions, hyperventilation pursuant to anxiety, or exposure to neurotoxins. We analyzed data from community members exposed to the World Trade Center (WTC) disaster of September 11, 2001, to evaluate whether exposure to the disaster was associated with paresthesias. Methods: Analysis of data from 3141 patients of the WTC Environmental Health Center. Results: Fifty-six percent of patients reported paresthesias at enrollment 7 to 15 years following the WTC disaster. After controlling for potential confounders, paresthesias were associated with severity of exposure to the WTC dust cloud and working in a job requiring cleaning of WTC dust. Conclusions: This study suggests that paresthesias were commonly associated with WTC-related exposures or post-WTC cleaning work. Further studies should objectively characterize these paresthesias and seek to identify relevant neurotoxins or paresthesia-inducing activities.
Angiogenic factor imbalance precedes complement deposition in placentae of the BPH/5 model of preeclampsia

Preeclampsia (PE), a hypertensive disorder of pregnancy, is a leading cause of maternal and fetal morbidity and mortality. Although the etiology is unknown, PE is thought to be caused by defective implantation and decidualization in pregnancy. Pregnant blood pressure high (BPH)/5 mice spontaneously develop placentopathies and maternal features of human PE. We hypothesized that BPH/5 implantation sites have transcriptomic alterations. Next‐generation RNA sequencing of implantation sites at peak decidualization, embryonic day (E)7.5, revealed complement gene up‐regulation in BPH/5 vs. controls. In BPH/5, expression of complement factor 3 was increased around the decidual vasculature of E7.5 implantation sites and in the trophoblast giant cell layer of E10.5 placentae. Altered expression of VEGF pathway genes in E5.5 BPH/5 implantation sites preceded complement dysregulation, which correlated with abnormal vasculature and increased placental growth factor mRNA and VEGF164 expression at E7.5. By E10.5, proangiogenic genes were down‐regulated, whereas antiangiogenic sFlt‐1 was up‐regulated in BPH/5 placentae. We found that early local misexpression of VEGF genes and abnormal decidual vasculature precededs Flt‐1 over expression and increased complement deposition in BPH/5 placentae. Our findings suggest that abnormal decidual angiogenesis precedes complement activation, which in turn contributes to the aberrant trophoblast invasion and poor placentation that underlie PE. —Sones, J. L. , Merriam, A. A. , Seffens, A. , Brown‐Grant, D. ‐A. , Butler, S. D. , Zhao, A. M. , Xu, X. , Shawber, C. J., Grenier, J. K. , Douglas, N. C. Angiogenic factor imbalance precedes complement deposition in placentae of the BPH/5 model of preeclampsia. FASEB J. 32, 2574–2586 (2018). www.fasebj. org
Dosage of the Abcg1-U2af1 Region Modifies Locomotor and Cognitive Deficits Observed in the Tc1 Mouse Model of Down Syndrome

Down syndrome (DS) results from one extra copy of human chromosome 21 and leads to several alterations including intellectual disabilities and locomotor defects. The transchromosomic Tc1 mouse model carrying an extra freely-segregating copy of human chromosome 21 was developed to better characterize the relation between genotype and phenotype in DS. The Tc1 mouse exhibits several locomotor and cognitive deficits related to DS. In this report we analyzed the contribution of the genetic dosage of 13 conserved mouse genes located between Abcg1 and U2af1, in the telomeric part of Hsa21. We used the Ms2Yah model carrying a deletion of the corresponding interval in the mouse genome to rescue gene dosage in the Tc1/Ms2Yah compound mice to determine how the different behavioral phenotypes are affected. We detected subtle changes with the Tc1/Ms2Yah mice performing better than the Tc1 individuals in the reversal paradigm of the Morris water maze. We also found that Tc1/Ms2Yah compound mutants performed better in the rotarod than the Tc1 mice. This data support the impact of genes from the Abcg1-U2af1 region as modifiers of Tc1-dependent memory and locomotor phenotypes. Our results emphasize the complex interactions between triplicated genes inducing DS features.
Residual Gas in the Vacuum System of the Solaris 1.5GeV Electron Storage Ring

Solaris is a third generation light source constructed at the Jagiellonian University in Krakow, Poland. The machine was designed by the MAX IV Laboratory team. The replica of the 1.5 GeV storage ring with 96 m circumference of a vacuum system was successfully built and now the synchrotron facility is after the 3 phase of commissioning. Recent installation of the Residual Gas Analyzer (RGA) in the storage ring allows now for evaluation of the residual gas composition. Within this paper the result of residual gas analysis in the vacuum system of storage ring during different states of the machine will be presented. Result of vacuum performance regarding beam cleaning and beam lifetime will be presented. Moreover, the NEG strips performance will be evaluated and reported. VACUUM SYSTEM OF THE STORAGE RING The Solaris storage ring is composed of twelve double bend achromat (DBA) cells and twelve straight sections with circumference of 96 m [1]. The 1 straight section is for injection and diagnostic, the 3 straight contains a dipole kicker [2] and in the 12 straight RF system is installed [3]. The DBA vacuum chamber has inner dimensions of 40x20 mm (horizontal/vertical). Figure 1: Vacuum chamber of the arc section. However, in the DBA centre the aperture is increased up to 56x28 mm. This chamber contains two Non Evaporable Getter (NEG) strips ST707 (Zr-V-Fe), three differential diode Sputter Ion Pumps (SIPs) and one Titanium Sublimation Pump (TSP). To absorb synchrotron radiation power each arc vacuum chamber contains three crotch absorbers, one end absorber (HAA) and two distributed absorbers. A standard straight section vacuum chamber includes two SIPs and one crotch absorber (see Fig. 2). One arc vacuum chamber and one straight with three valves define one vacuum sector in the Solaris storage ring. Figure 2: Vacuum chamber of the straight section. The nominal pumping speed of SIPs for N2 is around 6660 l/s whereas the nominal pumping speed of NEGs combined with TSPs for H2 is around 27850 l/s [4]. Two Cold Cathode Vacuum Gauge (CCVG) have been recently installed in the machine. First in the transfer line and second in the storage ring in the 1 straight section together with the residual gas analyser. To evaluate progress of the conditioning process the average pressure in the storage ring was estimated based on ion currents from SIPs.
Match-derived relative pitch area changes the physical and team tactical performance of elite soccer players in small-sided soccer games

ABSTRACT Small-sided games (SSGs) are used in training sessions to prepare for full-sized matches. For the same number of players, smaller pitch sizes result in decreased physical performance and shorter interpersonal distances. A relative pitch area derived from the full-sized match results in larger pitch sizes and this may increase the fit between SSGs and full-sized matches. This study aimed to investigate SSGs with a traditional small pitch and a match-derived relative pitch area in youth elite soccer players. Four age categories (under-13, under-15, under-17 and under-19) played 4 vs. 4 plus goalkeepers on a small (40x30m, 120m2 relative pitch area) and large pitch (68x47m, 320m2 relative pitch area). The number of games per age category ranged 15–30. Positional data (LPM-system) were collected to determine physical (total distance covered, high intensity distance and number of sprints) and team tactical (inter-team distance, LPW-ratio, surface area, stretch indices, goalkeeper-defender distance) performance measures and tactical variability. On a large pitch, physical performance significantly increased, inter-team and intra-team distances were significantly larger and tactical variability of intra-team distance measures significantly increased. The match-derived relative pitch area is an important training manipulation and leads to changes in physical and tactical performance 4 vs. 4 plus goalkeepers.
The pseudogene-derived long non-coding RNA SFTA1P suppresses cell proliferation, migration, and invasion in gastric cancer

Pseudogenes were once regarded as transcriptionally inactive and without specific molecular function. However, current evidence shows that pseudogene-derived long non-coding RNAs (lncRNAs) may be crucial regulators of human cancer development, including gastric cancer (GC). In the present study, we report that a pseudogene-derived lncRNA named surfactant associated 1, pseudogene (SFTA1P), which is 693-nt long, was significantly down-regulated in GC tissues compared with that in the adjacent normal tissues. In addition, decreased SFTA1P expression was strongly correlated with advanced tumor lymph node metastasis (TNM) stage, larger tumor size, lymphatic metastasis, and poor prognosis of patients with GC. Moreover, gain-of-function experiments revealed that the overexpression of SFTA1P inhibits cell proliferation, migration, and invasion, thus verifying the tumor inhibitory role of SFTA1P in GC. Furthermore, we investigated the potential action mechanism of SFTA1P. Our results showed that down-regulation of SFTA1P may be associated with decreased TP53 expression. In summary, our work suggests that the pseudogene-derived lncRNA SFTA1P functions as a tumor suppressor in GC and thus may act as a potential diagnostic and therapeutic target of GC.
Brain Activation Patterns in Response to Conspecific and Heterospecific Social Acoustic Signals in Female Plainfin Midshipman Fish, Porichthys notatus

While the peripheral auditory system of fish has been well studied, less is known about how the fish’s brain and central auditory system process complex social acoustic signals. The plainfin midshipman fish, Porichthys notatus, has become a good species for investigating the neural basis of acoustic communication because the production and reception of acoustic signals is paramount for this species’ reproductive success. Nesting males produce long-duration advertisement calls that females detect and localize among the noise in the intertidal zone to successfully find mates and spawn. How female midshipman are able to discriminate male advertisement calls from environmental noise and other acoustic stimuli is unknown. Using the immediate early gene product cFos as a marker for neural activity, we quantified neural activation of the ascending auditory pathway in female midshipman exposed to conspecific advertisement calls, heterospecific white seabass calls, or ambient environment noise. We hypothesized that auditory hindbrain nuclei would be activated by general acoustic stimuli (ambient noise and other biotic acoustic stimuli) whereas auditory neurons in the midbrain and forebrain would be selectively activated by conspecific advertisement calls. We show that neural activation in two regions of the auditory hindbrain, i.e., the rostral intermediate division of the descending octaval nucleus and the ventral division of the secondary octaval nucleus, did not differ via cFos immunoreactive (cFos-ir) activity when exposed to different acoustic stimuli. In contrast, female midshipman exposed to conspecific advertisement calls showed greater cFos-ir in the nucleus centralis of the midbrain torus semicircularis compared to fish exposed only to ambient noise. No difference in cFos-ir was observed in the torus semicircularis of animals exposed to conspecific versus heterospecific calls. However, cFos-ir was greater in two forebrain structures that receive auditory input, i.e., the central posterior nucleus of the thalamus and the anterior tuberal hypothalamus, when exposed to conspecific calls versus either ambient noise or heterospecific calls. Our results suggest that higher-order neurons in the female midshipman midbrain torus semicircularis, thalamic central posterior nucleus, and hypothalamic anterior tuberal nucleus may be necessary for the discrimination of complex social acoustic signals. Furthermore, neurons in the central posterior and anterior tuberal nuclei are differentially activated by exposure to conspecific versus other acoustic stimuli.
Linear Rayleigh-Taylor Instability for Viscous, Compressible Fluids

We study the equations obtained from linearizing the compressible Navier–Stokes equations around a steady-state profile with a heavier fluid lying above a lighter fluid along a planar interface, i.e., a Rayleigh–Taylor instability. We consider the equations with or without surface tension, with the viscosity allowed to depend on the density, in both periodic and nonperiodic settings. In the presence of viscosity there is no natural variational framework for constructing growing mode solutions to the linearized problem. We develop a general method of studying a family of modified variational problems in order to produce maximal growing modes. Using these growing modes, we construct smooth (when restricted to each fluid domain) solutions to the linear equations that grow exponentially in time in Sobolev spaces. We then prove an estimate for arbitrary solutions to the linearized equations in terms of the fastest possible growth rate for the growing modes. In the periodic setting, we show that sufficiently sm.