Miracle-dz/UniFAR-FTUs huggingface dataset:
Paleolimnological Signatures from Carbon and Oxygen Isotopic Ratios in Carbonates, from Organic Carbon-Rich Lacustrine Sediments: Chapter 6

Primary and early diagenetic carbonate minerals may be associated with organic carbon-rich lacustrine sediments. The stable oxygen and carbon isotopic compositions of these carbonates can yield useful paleoenvironmental information. Primary carbonates from hydrologically open lakes typically show little or only poorly correlated covariance between oxygen and carbon isotopic variations, whereas carbonates precipitated from surface waters of closed lakes display characteristic, highly correlated covariance. Oxygen isotopic ratios in early diagenetic phases reflect the isotopic composition of the waters in which the host sediments were deposited. The carbon isotopic composition of diagenetic carbonates is determined by the nature of the dominant microbiological processes inv lved in diagenesis of organic matter during the earliest stages of burial. In lakes poor in dissolved sulfate, bacterial methanogenesis is dominant and produces carbonates with markedly positive 13C values. Sulfate-rich lakes favor bacterial sulfate reduction that leads to precipitation of carbonates with negative 13C signatures. Using isotopic data from carbonates from Lake Bosumtwi, Ghana, as a case study, we show that characteristic relationships exist between isotopic compositions of primary and diagenetic carbonates of sulfate-poor and sulfate-rich lakes.
A model for the termination of the Ryukyu subduction zone against Taiwan: A junction of collision, subduction/separation, and subduction boundaries

[1] The NW moving Philippine Sea plate (PSP) collides with the Eurasian plate (EUP) in the vicinity of Taiwan, and at the same time, it subducts toward the north along SW Ryukyu. The Ryukyu subduction zone terminates against eastern Taiwan. While the Ryukyu Trench is a linear bathymetric low about 100 km east of Taiwan, closer to Taiwan, it cannot be clearly identified bathymetrically owing to the deformation related to the collision, making the location of the intersection of the Ryukyu with Taiwan difficult to decipher. We propose a model for this complex of boundaries on the basis of seismicity and 3-D velocity structures. In this model the intersection is placed at the latitude of about 23.7°N, placing the northern part of the Coastal Range on EUP. As PSP gets deeper along the subduction zone it collides with EUP on the Taiwan side only where they are in direct contact. Thus, the Eurasian plate on the Taiwan side is being pushed and compressed by the NW moving Philippine Sea plate, at increasing depth toward the north. Offshore of northeastern Taiwan the wedge-shaped EUP on top of the Ryukyu subducting plate is connected to the EUP on the Ryukyu side and coupled to the NW moving PSP by friction at the plate interface. The two sides of the EUP above the western end of the subduction zone are not subjected to the same forces, and a difference in motions can be expected. The deformation of Taiwan as revealed by continuous GPS measurements, geodetic movement along the east coast of Taiwan, and the formation of the Hoping Basin can be understood in terms of the proposed model.
The long non-coding RNA Paupar regulates the expression of both local and distal genes

Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome‐wide independently of their sites of synthesis. Here, we describe the genomically local and more distal functions of Paupar, a vertebrate‐conserved and central nervous system‐expressed lncRNA transcribed from a locus upstream of the gene encoding the PAX6 transcription factor. Knockdown of Paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neural differentiation. Paupar acts in a transcript‐dependent manner both locally, to regulate Pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with PAX6 protein. Paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is modulated by Paupar transcript levels. Our findings demonstrate that a lncRNA can function in trans at transcriptional regulatory elements distinct from its site of synthesis to control large‐scale transcriptional programmes.
Lymphocytes eject interferogenic mitochondrial DNA webs in response to CpG and non-CpG oligodeoxynucleotides of class C

Significance Release of pathogen- and danger-associated molecular patterns (PAMPs and DAMPs) contributes to inflammatory responses and antiviral signaling. Mitochondrial DNA (mtDNA) is a potent DAMP molecule observed in blood circulation of trauma, autoimmune, HIV, and certain cancer patients. Here, we report a previously unrecognized lymphocyte feature that CpG and non-CpG oligodeoxynucleotides of class C promptly induce release of mtDNA as extracellular web-like structures. Lymphocyte mtDNA webs provoked antiviral type I IFN production in peripheral blood mononuclear cells but were devoid of bactericidal proteins. Notably, cells remained viable after the release. Our findings imply an alternative role for lymphocytes in antiviral signaling by utilizing their mtDNA as a rapid signaling molecule to communicate danger. Circulating mitochondrial DNA (mtDNA) is receiving increasing attention as a danger-associated molecular pattern in conditions such as autoimmunity, cancer, and trauma. We report here that human lymphocytes [B cells, T cells, natural killer (NK) cells], monocytes, and neutrophils derived from healthy blood donors, as well as B cells from chronic lymphocytic leukemia patients, rapidly eject mtDNA as web filament structures upon recognition of CpG and non-CpG oligodeoxynucleotides of class C. The release was quenched by ZnCl2, independent of cell death (apoptosis, necrosis, necroptosis, autophagy), and continued in the presence of TLR9 signaling inhibitors. B-cell mtDNA webs were distinct from neutrophil extracellular traps concerning structure, reactive oxygen species (ROS) dependence, and were devoid of antibacterial proteins. mtDNA webs acted as rapid (within minutes) messengers, priming antiviral type I IFN production. In summary, our findings point at a previously unrecognized role for lymphocytes in antimicrobial defense, utilizing mtDNA webs as signals in synergy with cytokines and natural antibodies, and cast light on the interplay between mitochondria and the immune system.
Effect of seepage on sediment transport

This study presents the experimental results and theoretical analyses of seepage effects on sediment transport. A total of 529 experiments grouped under four different series of tests were conducted in a laboratory flume with a permeable sediment boundary to investigate the effect of seepage, the length of the suction zone and time on bedload transport rate. Two different types of cohesionless sand particles with diameters = 0.9 mm and 0.48 mm were used in the study. Three dimensionless groups, viz. Einstein’s parameter Φ, Shields’ parameter without seepage τ*o and modified densimetric Froude number Ω are chosen to examine how seepage affects bedload transport rate. Eleven undisturbed flow conditions were tested, five under clear water and six in live-bed condition. No bedforms with significant height were observed during the experiments. The results show that an increase in suction rate causes an increase in shear velocity excess, which is defined as the difference between the bed and critical shear velocities, leading to an increase in bedload transport rate. The experimental data also show that for the same undisturbed flow conditions, the dimensionless bedload transport rate increases linearly (in semi-logarithmic scale) with increasing suction rates. The equations for predicting bedload transport rate under suction are derived empirically; the predicted results using these empirical equations compared well with measured data, with an accuracy of ±20%. Published results from other researchers are used to compare with results obtained and inference drawn from the present study. The similarities and differences of these studies are highlighted. On the other hand, the experimental results show that the sediment transport rate decreases with an increase in injection velocity, but the magnitude of the reduction viii ATTENTION: The Singapore Copyright Act applies to the use of this document. Nanyang Technological University Library
Adhesion of 8701-BC breast cancer cells to type V collagen and 67 kDa receptor.

Ductal infiltration carcinomas (d.i.c.) of the breast are potentially highly metastatic tumours, associated with drastic alterations of the architecture and molecular composition of the extracellular matrix at the tumour-host interface. 8701-BC, a recently characterized cell line, isolated from primary d.i. c. , was used to study different aspects of tumor cell-substratum interactions. Since type V collagen deposition is augmented in d.i. c. we have examined the ability of 8701-BC cells to interact with this collagen species. We have found that cell binding to type V collagen was mediated by protein homologous to the 67 kDa laminin receptor (67-R). This conclusion is substantiated by the following observations: (a) a major band having an apparent molecular mass of 67 kDa and immunoreactive to the anti-67 R antibody was detectable by SDS-PAGE of the membrane proteins; (b) the antibody inhibited cellular adhesion to type V collagen in a dose-dependent way; (c) membrane proteins purified by affinity chromatography on type V collagen were immunoreactive to anti-67 R antibody, but not to anti-VLA1, VLA2 and VLA3 integrin antibodies. This receptor appears to have prominent carbohydrate-binding properties, since lactose competes with cell adhesion to type V collagen.
Deferred stent implantation in patients with ST-segment elevation myocardial infarction: a pilot study.

AIMS Disturbance in the flow of an infarct-related artery due to embolisation of thrombus and plaque material occurs frequently during primary percutaneous coronary intervention (PCI) and is associated with impaired prognosis. The aim of the present study was to minimise the risk of embolisation during PCI in patients with ST-segment elevation myocardial infarction (STEMI). METHODS AND RESULTS Of 124 consecutive patients with STEMI, thrombectomy and/or balloon dilatation was performed in 110 (89%). Stent implantation was deferred in 113 (91%) patients who then comprised the study group. In 38% of the patients stent implantation was deemed unnecessary at the second examination because of <30% residual stenosis and no visible thrombus, and all lesions re-examined three months later were patent. Major adverse cardiac events occurred in two patients during eight months of follow-up (one cardiac death, one case of reinfarction with target lesion revascularisation). In five patients no PCI was performed at all. Myocardial salvage determined by cardiac magnetic resonance in a subset of patients was relatively high. CONCLUSIONS Deferred stent implantation is safe in the majority of patients with STEMI. Although the concept has to be evaluated in a randomised trial, the strategy may prove beneficial for many patients referred for primary PCI.
Security Enhancement for Multiple Multi-Antenna Relaying Networks

In this paper, we investigate the secrecy performance of the multi-antenna relaying networks over Rayleigh fading channels, by taking the reliability of the first link spanning the transmitter to the relays into consideration. To improve the secrecy performance, two secure transmission strategies are designed at relays, namely, 1) Maximal ratio combining/Transmitter antenna selection (MRC/TAS) and 2) MRC/Maximal ratio transmission (MRC/MRT), assisted by a friendly jammer. Specifically, in order to present the advantages of the two proposed schemes, we derive the exact closed-form expressions of the outage probability (OP) and intercept probability (IP) to evaluate the security-reliability tradeoff (SRT) of the considered system, respectively. From our theoretical analysis as well as simulation results, we find that a) our proposed schemes outperform the conventional scheme with no cooperative jammer (CJ), and b) the MRT scheme is superior to the TAS one conditioned on the same set of system parameters.
Tropical Pacific baroclinic mode contribution and associated long waves for the 1994-1999 period from an assimilation experiment with altimetric data

[1] An Ocean General Circulation Model (OGCM) of the tropical Pacific in which combined TOPEX/Poseidon and ERS sea level anomalies are assimilated over January 1994 through July 1999, is used to investigate equatorial wave characteristics during the intense 1997–1999 El Nino-La Nina event. Near the equator, the linear vertical modes are estimated at each grid point of the OGCM simulation with and without assimilation. Consistently with an increase of the vertical gradient within the thermocline and a rise of the thermocline depth in the eastern basin, the assimilation results in an increased contribution of the higher-order baroclinic modes in the eastern basin and a decreased contribution of the first baroclinic mode in the western Pacific for the zonal current variability. For pressure, the first baroclinic mode contribution is reduced whereas the higher-order modes contribution is weakly impacted. Kelvin and first-meridional Rossby waves are then derived for the first two more energetic baroclinic modes in the simulation with assimilation. Kelvin waves of both modes constructively contribute to the strong warming observed in 1997, with the first (second) baroclinic mode being more energetic than the second (first) baroclinic mode in the early (mature) stage of the warming. Kelvin waves of both modes reflect as first meridional Rossby waves at the eastern boundary (reflection efficiency of ∼95%) and contribute to push back the warm pool westward. The reversal of the warming is apparently initiated by the second baroclinic mode contribution which controls the position of the 28°C isotherm in the surface layer in the far eastern Pacific from January 1998. At the western boundary, reflections of Rossby waves take place for both modes with an estimated total efficiency of ∼50% at 165°E. This suggests that, in our model, the delayed oscillator theory is not applicable for explaining the reversal from warm to cold conditions in 1998 while the zonal advective feedback was at work. More generally, the study suggests that it is necessary to take into account the vertical structure of the ocean when interpreting altimetric data, which can be done through an assimilation experiment.
Low-Cost PCB-Integrated 10-Gb/s Optical Transceiver Built With a Novel Integration Method

A novel integration method for the production of cost-effective optoelectronic printed circuit boards (OE PCBs) is presented. The proposed integration method allows fabrication of OE PCBs with manufacturing processes common to the electronics industry while enabling direct attachment of electronic components onto the board with solder reflow processes as well as board assembly with automated pick-and-place tools. The OE PCB design is based on the use of polymer multimode waveguides, end-fired optical coupling schemes, and simple electro-optic connectors, eliminating the need for additional optical components in the optical layer, such as micro-mirrors and micro-lenses. A proof-of-concept low-cost optical transceiver produced with the proposed integration method is presented. This transceiver is fabricated on a low-cost FR4 substrate, comprises a polymer Y-splitter together with the electronic circuitry of the transmitter and receiver modules and achieves error-free 10-Gb/s bidirectional data transmission. Theoretical studies on the optical coupling efficiencies and alignment tolerances achieved with the employed end-fired coupling schemes are presented while experimental results on the optical transmission characteristics, frequency response, and data transmission performance of the integrated optical links are reported. The demonstrated optoelectronic unit can be used as a front-end optical network unit in short-reach datacommunication links.
A neuron autonomous role for the familial dysautonomia gene ELP1 in sympathetic and sensory target tissue innervation

Familial dysautonomia (FD) is characterized by severe and progressive sympathetic and sensory neuron loss caused by a highly conserved germline point mutation of the human ELP1/IKBKAP gene. Elp1 is a subunit of the hetero-hexameric transcriptional elongator complex, but how it functions in disease-vulnerable neurons is unknown. Conditional knockout mice were generated to characterize the role of Elp1 in migration, differentiation and survival of migratory neural crest (NC) progenitors that give rise to sympathetic and sensory neurons. Loss of Elp1 in NC progenitors did not impair their migration, proliferation or survival, but there was a significant impact on post-migratory sensory and sympathetic neuron survival and target tissue innervation. Ablation of Elp1 in post-migratory sympathetic neurons caused highly abnormal target tissue innervation that was correlated with abnormal neurite outgrowth/branching and abnormal cellular distribution of soluble tyrosinated α-tubulin in Elp1-deficient primary sympathetic and sensory neurons. These results indicate that neuron loss and physiologic impairment in FD is not a consequence of abnormal neuron progenitor migration, differentiation or survival. Rather, loss of Elp1 leads to neuron death as a consequence of failed target tissue innervation associated with impairments in cytoskeletal regulation.
Cerebrospinal Fluid (CSF) Neuronal Biomarkers across the Spectrum of HIV Infection: Hierarchy of Injury and Detection

The character of central nervous system (CNS) HIV infection and its effects on neuronal integrity vary with evolving systemic infection. Using a cross-sectional design and archived samples, we compared concentrations of cerebrospinal fluid (CSF) neuronal biomarkers in 143 samples from 8 HIV-infected subject groups representing a spectrum of untreated systemic HIV progression and viral suppression: primary infection; four groups of chronic HIV infection neuroasymptomatic (NA) subjects defined by blood CD4+ T cells of >350, 200–349, 50–199, and <50 cells/µL; HAD; treatment-induced viral suppression; and ‘elite’ controllers. Samples from 20 HIV-uninfected controls were also examined. The neuronal biomarkers included neurofilament light chain protein (NFL), total and phosphorylated tau (t-tau, p-tau), soluble amyloid precursor proteins alpha and beta (sAPPα, sAPPβ) and amyloid beta (Aβ) fragments 1–42, 1–40 and 1–38. Comparison of the biomarker changes showed a hierarchy of sensitivity in detection and suggested evolving mechanisms with progressive injury. NFL was the most sensitive neuronal biomarker. Its CSF concentration exceeded age-adjusted norms in all HAD patients, 75% of NA CD4<50, 40% of NA CD4 50–199, and 42% of primary infection, indicating common neuronal injury with untreated systemic HIV disease progression as well as transiently during early infection. By contrast, only 75% of HAD subjects had abnormal CSF t-tau levels, and there were no significant differences in t-tau levels among the remaining groups. sAPPα and β were also abnormal (decreased) in HAD, showed less marked change than NFL with CD4 decline in the absence of HAD, and were not decreased in PHI. The CSF Aβ peptides and p-tau concentrations did not differ among the groups, distinguishing the HIV CNS injury profile from Alzheimer's disease. These CSF biomarkers can serve as useful tools in selected research and clinical settings for patient classification, pathogenetic analysis, diagnosis and management.
the Phagosome Independent Targeting Mechanism of Rac to and Phagocytosis: Positive Charge-Dependent R-Mediated g Mechanism of Rac during Fc Isoform-Specific Membrane Targeting

Rac1 and Rac2 are capable of stimulating superoxide production in vitro, but their targeting and functional mechanisms are still unknown. In the present study, we found that Rac1, 2, and 3 all accumulate at the phagosome during Fc (cid:1) R-mediated phagocytosis, and that the order of accumulation (Rac1 > Rac3 > Rac2) depends on the net positive charge in their polybasic (PB) regions (183–188 aa). Although all GFP-tagged prenylated PB regions of Rac isoforms (GFP-Rac(PB)) and GFP-tagged prenylated 6 Ala (GFP-6A) accumulated during phagocytosis, GFP-Rac2(PB) and GFP-6A showed weak accumulation at the phagosome through a linear structure connecting the phagosome and endomembranes. The PB region of Rac1 showed strong phospholipid interaction with PI(3)P, PI(4)P, PI(5)P, PI(3,4,5)P 3, and phosphatidic acid, however, that of Rac2 did not. Constitutively active Rac2, GFP-Rac2(Q61L), was predominantly localized at the endomembranes; these endomembranes fused to the phagosome through the linear structure during phagocytosis, and this accumulation mechanism did not depend on positive charge in the PB region. Our conclusion is that Rac1 directly targets to the phagosome using the positively charged PB region and this accumulation mechanism is likely enhanced by the phospholipids. In addition to this mechanism, Rac2
Potential for long‐term transfer of dissolved organic carbon from riparian zones to streams in boreal catchments

Boreal regions store most of the global terrestrial carbon, which can be transferred as dissolved organic carbon (DOC) to inland waters with implications for both aquatic ecology and carbon budgets. Headwater riparian zones (RZ) are important sources of DOC, and often just a narrow ‘dominant source layer’ (DSL) within the riparian profile is responsible for most of the DOC export. Two important questions arise: how long boreal RZ could sustain lateral DOC fluxes as the sole source of exported carbon and how its hydromorphological variability influences this role. We estimate theoretical turnover times by comparing carbon pools and lateral exports in the DSL of 13 riparian profiles distributed over a 69 km2 catchment in northern Sweden. The thickness of the DSL was 36 ± 18 (average ± SD) cm. Thus, only about one‐third of the 1‐m‐deep riparian profile contributed 90% of the lateral DOC flux. The 13 RZ exported 8.7 ± 6.5 g C m−2 year−1, covering the whole range of boreal stream DOC exports. The variation could be explained by local hydromorphological characteristics including RZ width (R2 = 0.90). The estimated theoretical turnover times were hundreds to a few thousands of years, that is there is a potential long‐lasting supply of DOC. Estimates of net ecosystem production in the RZ suggest that lateral fluxes, including both organic and inorganic C, could be maintained without drawing down the riparian pools. This was supported by measurements of stream DO14C that indicated modern carbon as the predominant fraction exported, including streams disturbed by ditching. The transfer of DOC into boreal inland waters from new and old carbon sources has a major influence on surface water quality and global carbon balances. This study highlights the importance of local variations in RZ hydromorphology and DSL extent for future DOC fluxes under a changing climate.