Miracle-dz/UniFAR-FTUs huggingface dataset:
Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling

ABSTRACT Corals continuously adjust to short-term variation in light availability on shallow reefs. Long-term light alterations can also occur as a result of natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short-term photophysiological responses are relatively well understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species, Acropora muricata. High light (HL)- and low light (LL)-acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ. Rapid light curves using pulse-amplitude modulation (PAM) fluorometry revealed photophysiological acclimation of LL corals to HL and HL corals to LL within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL corals than for their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability. Summary: PAM fluorometry indicates rapid acclimation of corals to high and low light. In contrast, metabolomics reveals possible stress under high light and a lack of rapid adjustment under low light.
The Effect of Green and Black Tea Polyphenols on BRCA2 Deficient Chinese Hamster Cells by Synthetic Lethality through PARP Inhibition

Tea polyphenols are known antioxidants presenting health benefits due to their observed cellular activities. In this study, two tea polyphenols, epigallocatechin gallate, which is common in green tea, and theaflavin, which is common in black tea, were investigated for their PARP inhibitory activity and selective cytotoxicity to BRCA2 mutated cells. The observed cytotoxicity of these polyphenols to BRCA2 deficient cells is believed to be a result of PARP inhibition induced synthetic lethality. Chinese hamster V79 cells and their BRCA2 deficient mutant V-C8, and V-C8 with gene complemented cells were tested against epigallocatechin gallate and theaflavin. In addition, Chinese hamster ovary (CHO) wild-type cells and rad51D mutant 51D1 cells were used to further investigate the synthetic lethality of these molecules. The suspected PARP inhibitory activity of epigallocatechin and theaflavin was confirmed through in vitro and in vivo experiments. Epigallocatechin gallate showed a two-fold increase of cytotoxicity to V-C8 cells compared to V79 and gene complimented cells. Compared to CHO wild type cells, 51D1 cells also showed elevated cytotoxicity following treatment with epigallocatechin gallate. Theaflavin, however, showed a similar increase of cytotoxicity to VC8 compared to V79 and gene corrected cells, but did not show elevation of cytotoxicity towards rad51D mutant cells compared to CHO cells. Elevation of sister chromatid exchange formation was observed in both tea polyphenol treatments. Polyphenol treatment induced more micronuclei formation in BRCA2 deficient cells and rad51D deficient cells when compared against the respective wild type cells. In conclusion, tea polyphenols, epigallocatechin gallate, and theaflavin may present selective cytotoxicity to BRCA2 deficient cells through synthetic lethality induced by PARP inhibition.
Predictors of Lymphoceles in Women Who Underwent Laparotomic Retroperitoneal Lymph Node Dissection for Early Gynecologic Cancer: A Retrospective Cohort Study

Background: Lymphoceles could represent a detrimental complication after retroperitoneal lymph node dissection. Our aim was to elucidate predictors of lymphoceles. Methods: Between 2011 and 2017, medical records of consecutive women who underwent laparotomic retroperitoneal lymph node dissection for FIGO stage I or II gynecologic cancer were reviewed. Results: A total of 204 women, including those with lymphoceles (n = 31) and symptomatic lymphoceles (n = 7), were reviewed. According to multivariable analysis, parity (odds ratio = 0.59, p = 0.003), adjuvant pelvic radiotherapy (odds ratio = 2.60, p = 0.039), and peritoneal nonclosure without pelvic drainage (odds ratio = 2.31, p = 0.048) were predictors of lymphoceles. In addition, parity (odds ratio = 0.73, p = 0.03), hypertension (odds ratio = 2.62, p = 0.02), and peritoneal partial closure with pelvic drainage (odds ratio = 0.27, p = 0.02) were predictors of complications. Conclusion: Low parity, adjuvant pelvic radiotherapy, and peritoneal nonclosure without pelvic drainage were associated with increased lymphocele formation. In addition, a lower complication rate was found in the peritoneal partial closure with pelvic drainage group; thus, peritoneal partial closure with pelvic drainage might be suggested for women who undergo laparotomic retroperitoneal lymph node dissection.
Effect of phenytoin on the pharmacokinetics of efavirenz in rabbits

Phenytoin is an inducer of the CYP3A4 and CYP2B6. Efavirenz is a substrate of the CYP3A4 and CYP2B6. Co-adminstration of both drugs may result in changes of efavirenz pharmacokinetics. The aim of this study was to investigate the effect of phenytoin on the pharmacokinetic of efavirenz in rabbits. Ten male rabbits were randomly assigned into a 2-period pharmacokinetic study with a 14 days washout period in a crossover design. In period 1, 5 rabbits in group 1 received efavirenz 70 mg/kg orally. In group 2, another 5 rabbits received phenytoin 30 mg/kg once daily orally for 7 days, followed by efavirenz 70 mg/kg on day 7. In period 2, the 2 groups were treated in reverse. Blood samples were collected at 0, 0.5, 1, 2, 4, 8, 12, 24, 48, 72, 96 h after each treatment. Phenytoin significantly decreased the AUC0-96 , AUC0∞ , Cmax and Tmax of efavirenz by 55.99% , 48.84% , 48.88% and 71.43%, respectively. The clearance of efavirenz was significantly increased by 101.47% whereas the t1/2 was not significantly decreased. Phenytoin increase efavirenz clearance probably via CYP3A4 and CYP2B6 induction.
“Gravity” - a new simple negative pressure wound therapy self-build design for low income countries

Abstract Negative Pressure Wound Therapy (NPWT) is prohibitively expensive at the moment and therefore not easily accessible in low-income countries. An additional problem is the requirement of consistent reliable electricity to power the devices. A new low-cost NPWT device was designed from low cost and simple materials and it can be built and operated following a simple set of instructions. The so-called Gravity device was made from parts costing just under £6 GBP (May 2016) and it creates a constant pressure of 125 mmHg. Gravity operated from 4 hours and 40 minutes up to 5 hours and 18 minutes before needing to be reset. This reset can be achieved without patient involvement. Gravity was taken to Kenya by a Doctor on 5 May 2016 to be evaluated. A NPWT device prototype was successfully made and positive feedback was received from Kenya.
Study on the Isolation of Two Atrazine-Degrading Bacteria and the Development of a Microbial Agent

Two bacteria capable of efficiently degrading atrazine were isolated from soil, and named ATLJ-5 and ATLJ-11. ATLJ-5 and ATLJ-11 were identified as Bacillus licheniformis and Bacillus megaterium, respectively. The degradation efficiency of atrazine (50 mg/L) by strain ATLJ-5 can reach about 98.6% after 7 days, and strain ATLJ-11 can reach 99.6% under the same conditions. The degradation of atrazine is faster when two strains are used in combination. Adding the proper amount of fresh soil during the degradation of atrazine by these two strains can also increase the degradation efficiency. The strains ATLJ-5 and ATLJ-11 have high tolerance to atrazine, and can tolerate at least 1000 mg/L of atrazine. In addition, the strains ATLJ-5 and ATLJ-11 have been successfully made into a microbial agent that can be used to treat atrazine residues in soil. The degradation efficiency of atrazine (50 mg/kg) could reach 99.0% by this microbial agent after 7 days. These results suggest that the strains ATLJ-5 and ATLJ-11 can be used for the treatment of atrazine pollution.
The metabolic cost of in vivo constant muscle force production at zero net mechanical work

ABSTRACT The metabolic cost per unit force is generally thought to increase with the mechanical work done by the muscle fibres. It is currently unclear how the metabolic cost of doing alternating positive and negative muscle fibre mechanical work relates to the metabolic cost of doing zero muscle fibre mechanical work at similar muscle force. The current study aimed to investigate this issue by comparing in vivo metabolic power between a dynamic and an isometric near-constant force production task. In both tasks, participants performed periodic movement about the knee joint in the gravitational field. Therefore, net external mechanical work was constrained to be zero. The tasks mainly differed from each other in average positive knee joint mechanical power, which was 4.3±0.5 W per leg during the dynamic task and 0.1±0.1 W per leg during the isometric task. Knee extension torque was near-constant around 15.2±1.7 N m during the dynamic task and around 15.7±1.7 N m during the isometric task. Owing to near-constant knee extension torque, quadriceps tendon length was presumably nearly constant during both tasks. Therefore, knee joint mechanical work was predominantly done by the muscle fibres in both tasks. Average gross metabolic power was 3.22±0.46 W kg−1 during the dynamic task and 2.13±0.36 W kg−1 during the isometric task. Because tasks differed mainly in the amount of positive muscle fibre mechanical work, these results imply that the metabolic cost of near-constant force production in vivo at zero net mechanical work can be reduced by minimizing positive muscle fibre mechanical work. Summary: For constant-torque isolated knee movements in the gravitational field, mean metabolic power is greater when positive muscle fibre mechanical work is substantial compared with when it is near zero.
A Dual-Modality Linker Enables Site-Specific Conjugation of Antibody Fragments for 18F-Immuno-PET and Fluorescence Imaging

Antibody-based dual-modality (PET/fluorescence) imaging enables both presurgery antigen-specific immuno-PET for noninvasive whole-body evaluation and intraoperative fluorescence for visualization of superficial tissue layers for image-guided surgery. Methods: We developed a universal dual-modality linker (DML) that facilitates site-specific conjugation to a cysteine residue–bearing antibody fragment, introduction of a commercially available fluorescent dye (via an amine-reactive prosthetic group), and rapid and efficient radiolabeling via click chemistry with 18F-labeled trans-cyclooctene (18F-TCO). To generate a dual-modality antibody fragment–based imaging agent, the DML was labeled with the far-red dye sulfonate cyanine 5 (sCy5), site-specifically conjugated to the C-terminal cysteine of the anti-prostate stem cell antigen (PSCA) cys-diabody A2, and subsequently radiolabeled by click chemistry with 18F-TCO. The new imaging probe was evaluated in a human PSCA-positive prostate cancer xenograft model by sequential immuno-PET and optical imaging. Uptake in target tissues was confirmed by ex vivo biodistribution. Results: We successfully synthesized a DML for conjugation of a fluorescent dye and 18F. The anti-PSCA cys-diabody A2 was site-specifically conjugated with either DML or sCy5 and radiolabeled via click chemistry with 18F-TCO. Immuno-PET imaging confirmed in vivo antigen-specific targeting of prostate cancer xenografts as early as 1 h after injection. Rapid renal clearance of the 50-kDa antibody fragment enables same-day imaging. Optical imaging showed antigen-specific fluorescent signal in PSCA-positive xenografts and high contrast to surrounding tissue and PSCA-negative xenografts. Conclusion: The DML enables site-specific conjugation away from the antigen-binding site of antibody fragments, with a controlled linker-to-protein ratio, and combines signaling moieties for 2 imaging systems into 1 molecule. Dual-modality imaging could provide both noninvasive whole-body imaging with organ-level biodistribution and fluorescence image–guided identification of tumor margins during surgery.
Development of a Modified Psoriatic Arthritis Disease Activity Score Using the Medical Outcomes Study Short Form 12 as a Measure of Quality of Life

The Psoriatic Arthritis Disease Activity Score (PASDAS) is a composite measure of psoriatic arthritis (PsA) disease activity. The length of its patient‐reported components raises concern about questionnaire burden. The PASDAS includes the Medical Outcomes Study Short Form 36 (SF‐36) health survey. We undertook this study to investigate the agreement between the PASDAS and a modified PASDAS (mPASDAS), which substituted the SF‐36 with the shortened SF‐12.
Microstructure and Mechanical Performance of Additively Manufactured Aluminum 2024-T3/Acrylonitrile Butadiene Styrene Hybrid Joints Using an AddJoining Technique

AddJoining is an emerging technique that combines the principles of the joining method and additive manufacturing. This technology is an alternative method to produce metal–polymer (composite) structures. Its viability was demonstrated for the material combination composed of aluminum 2024-T3 and acrylonitrile butadiene styrene to form hybrid joints. The influence of the isolated process parameters was performed using the one-factor-at-a-time approach, and analyses of variance were used for statistical analysis. The mechanical performance of single-lap joints varied from 910 ± 59 N to 1686 ± 39 N. The mechanical performance thus obtained with the optimized joining parameters was 1686 ± 39 N, which failed by the net-tension failure mode with a failure pattern along the 45° bonding line. The microstructure of the joints and the fracture morphology of the specimens were studied using optical microscopy and scanning electron microscopy. From the microstructure point of view, proper mechanical interlocking was achieved between the coated metal substrate and 3D-printed polymer. This investigation can be used as a base for further improvements on the mechanical performance of AddJoining hybrid-layered applications.
The Emerging Roles of TERRA in Telomere Maintenance and Genome Stability

The finding that transcription occurs at chromosome ends has opened new fields of study on the roles of telomeric transcripts in chromosome end maintenance and genome stability. Indeed, the ends of chromosomes are required to be protected from activation of DNA damage response and DNA repair pathways. Chromosome end protection is achieved by the activity of specific proteins that associate with chromosome ends, forming telomeres. Telomeres need to be constantly maintained as they are in a heterochromatic state and fold into specific structures (T-loops), which may hamper DNA replication. In addition, in the absence of maintenance mechanisms, chromosome ends shorten at every cell division due to limitations in the DNA replication machinery, which is unable to fully replicate the extremities of chromosomes. Altered telomere structure or critically short chromosome ends generate dysfunctional telomeres, ultimately leading to replicative senescence or chromosome instability. Telomere biology is thus implicated in multiple human diseases, including cancer. Emerging evidence indicates that a class of long noncoding RNAs transcribed at telomeres, known as TERRA for “TElomeric Repeat-containing RNA,” actively participates in the mechanisms regulating telomere maintenance and chromosome end protection. However, the molecular details of TERRA activities remain to be elucidated. In this review, we discuss recent findings on the emerging roles of TERRA in telomere maintenance and genome stability and their implications in human diseases.
Targeted next-generation sequencing detects rare genetic events in pheochromocytoma and paraganglioma

Background Knowing the genetic status of patients affected by paragangliomas and pheochromocytomas (PPGL) is important for the guidance of their management and their relatives. Our objective was to improve the diagnostic performances of PPGL genetic testing by next-generation sequencing (NGS). Methods We developed a custom multigene panel, which includes 17 PPGL genes and is compatible with both germline and tumour DNA screening. The NGS assay was first validated in a retrospective cohort of 201 frozen tumour DNAs and then applied prospectively to 623 DNAs extracted from leucocytes, frozen or paraffin-embedded PPGL tumours. Results In the retrospective cohort, the sensitivity of the NGS assay was evaluated at 100% for point and indels mutations and 86% for large rearrangements. The mutation rate was re-evaluated from 65% (132/202) to 78% (156/201) after NGS analysis. In the prospective cohort, NGS detected not only germline and somatic mutations but also co-occurring variants and mosaicism. A mutation was identified in 74% of patients for whom both germline and tumour DNA were available. Conclusion The analysis of 824 DNAs from patients with PPGL demonstrated that NGS assay significantly improves the performances of PPGL genetic testing compared with conventional methods, increasing the rate of identified mutations and identifying rare genetic mechanisms.
Clinical Outcomes and Clinico-pathological Correlations in Lupus Nephritis with Kidney Biopsy Showing Thrombotic Microangiopathy

Objective. Renal thrombotic microangiopathy (TMA) is an uncommon pathological finding in lupus nephritis (LN), and its clinical significance remains to be defined. Methods. Twenty-four patients with lupus nephritis (LN) and renal TMA were selected from a retrospective review of 677 biopsy-proven LN patients, and compared with 48 LN controls without TMA (1:2 ratio) matched according to demographics and treatments. Results. Renal TMA was noted in 3.5% of kidney biopsies of LN. TMA was associated with a higher prevalence of anti-Ro (45.8% vs 18.8%; p = 0.016), higher Systemic Lupus Erythematosus Disease Activity Index scores (21.4 ± 8.5 vs 10.8 ± 2.3; p < 0.001), lower estimated glomerular filtration rate (eGFR; 16.8 ± 11.7 ml/min vs 77.8 ± 28.6 ml/min; p < 0.001), and a higher percentage of patients who required dialysis (37.5% vs 2.1%; p < 0.001) at the time of kidney biopsy. Activity and chronicity indices [median (range)] were higher in the TMA group [11 (2–19) and 3 (1–8), respectively, compared with 7 (0–15) and 1 (0–3) in controls; p = 0.004 and p < 0.001; respectively]. Patients with TMA showed inferior 5-year renal survival and higher incidence of chronic kidney disease at last followup (70% and 66.6%, respectively, compared with 95% and 29.2% in controls; p = 0.023 and 0.002, respectively). The TMA group also showed lower median eGFR compared with controls [50.1 (IQR 7–132) ml/min vs 85.0 (IQR 12–147) ml/min; p = 0.003]. Five-year patient survival rate was similar between the 2 groups (87% and 98% in TMA and control group, respectively; p = 0.127). Conclusion. TMA in kidney biopsy was associated with more severe clinical and histological activity, and significantly inferior longterm renal outcome in LN.
Effectiveness of oral multiple sclerosis therapies in clinical context

Treatment of multiple sclerosis (MS) has undergone development unprecedented in neurology. With 14 therapeutic options now available to neurologists and their patients, making an accurate choice of the most suitable agent that will protect a patient's CNS from inflammatory damage is of paramount importance. In the absence of head-to-head randomized trials of most of the available therapies, studies using large longitudinal data collections from registries provide us with invaluable information about the relative effectiveness of immunotherapies in different contexts.
Analyzing digital politics: Challenges and experiments in a dual perspective

Social networks have become in the last decade central to political life. However, to those interested in analysing the communication strategies of parties and candidates at election time, the introduction of the Internet into the political sphere has proved a mixed blessing. Indeed, while retrieving, consulting, and archiving original documents pertaining to a specific campaign have become easier, faster, and achievable on a larger scale, thus opening up a promising El Dorado for research in this area, studying online campaigns has also inevitably introduced new technical, methodological and legal challenges which have turned out to be increasingly complex for academics in the humanities and social sciences to solve on their own.This paper therefore proposes to provide feedback on experience and experimental validation from a multidisciplinary project called POLIWEB devoted to the comparative analysis of political campaigns on social media in the run up to the 2014 elections to the European Parliament in France and in the United Kingdom. Together with observations from a humanities' perspective on issues related to such a project, this paper also presents experimental results concerning three of the data collection life cycle phases: collection, cleaning, and storage. The outcome is a data collection ready to be analysed for various purposes meant to address the political science topic under consideration.
Cloud-Edge Coordinated Processing: Low-Latency Multicasting Transmission

Recently, edge caching and multicasting arise as two promising technologies to support high-data-rate and low-latency delivery in wireless communication networks. In this paper, we design three transmission schemes aiming to minimize the delivery latency for cache-enabled multigroup multicasting networks. In particular, full caching bulk transmission scheme is first designed as a performance benchmark for the ideal situation where the caching capability of each enhanced remote radio head (eRRH) is sufficient large to cache all files. For the practical situation where the caching capability of each eRRH is limited, we further design two transmission schemes, namely partial caching bulk transmission (PCBT) and partial caching pipelined transmission (PCPT) schemes. In the PCBT scheme, eRRHs first fetch the uncached requested files from the baseband unit (BBU) and then all requested files are simultaneously transmitted to the users. In the PCPT scheme, eRRHs first transmit the cached requested files while fetching the uncached requested files from the BBU. Then, the remaining cached requested files and fetched uncached requested files are simultaneously transmitted to the users. The design goal of the three transmission schemes is to minimize the delivery latency, subject to some practical constraints. Efficient algorithms are developed for the low-latency cloud-edge coordinated transmission strategies. Numerical results are provided to evaluate the performance of the proposed transmission schemes and show that the PCPT scheme outperforms the PCBT scheme in terms of the delivery latency criterion.