Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types

To identify the transcriptional regulatory changes that are most widespread in solid tumors, we performed a pan-cancer analysis using over 600 pairs of tumors and adjacent normal tissues profiled in The Cancer Genome Atlas (TCGA). Frequency of upregulation was calculated across mRNA expression levels, microRNA expression levels and CpG methylation sites and is provided here as a resource. Frequent tumor-associated alterations were identified using a simple statistical approach. Many of the identified changes were consistent with the increased rate of cell division in cancer, such as the overexpression of cell cycle genes and hypermethylation of PRC2 binding sites. However, we also identified proliferation-independent alterations, which highlight novel pathways essential to tumor formation. Nearly all of the GABA receptors are frequently downregulated, with the gene encoding the delta subunit (GABRD) strongly upregulated as the notable exception. Metabolic genes are also frequently downregulated, particularly alcohol dehydrogenases and others consistent with the decreased role of oxidative phosphorylation in cancerous cells. Alterations in the composition of GABA receptors and metabolism may play a key role in the differentiation of cancer cells, independent of proliferation.
Effects of Seasonal Upwelling on Inorganic and Organic Matter Dynamics in the Water Column of Eastern Pacific Coral Reefs

The Gulf of Papagayo at the northern Pacific coast of Costa Rica experiences pronounced seasonal changes in water parameters caused by wind-driven coastal upwelling. While remote sensing and open water sampling already described the physical nature of this upwelling, the spatial and temporal effects on key parameters and processes in the water column have not been investigated yet, although being highly relevant for coral reef functioning. The present study investigated a range of water parameters on two coral reefs with different exposure to upwelling (Matapalo and Bajo Rojo) in a weekly to monthly resolution over one year (May 2013 to April 2014). Based on air temperature, wind speed and water temperature, three time clusters were defined: a) May to November 2013 without upwelling, b) December 2013 to April 2014 with moderate upwelling, punctuated by c) extreme upwelling events in February, March and April 2014. During upwelling peaks, water temperatures decreased by 7°C (Matapalo) and 9°C (Bajo Rojo) to minima of 20.1 and 15.3°C respectively, while phosphate, ammonia and nitrate concentrations increased 3 to 15-fold to maxima of 1.3 μmol PO4 3- L-1, 3.0 μmol NH4 + L-1 and 9.7 μmol NO3 - L-1. This increased availability of nutrients triggered several successive phytoplankton blooms as indicated by 3- (Matapalo) and 6-fold (Bajo Rojo) increases in chlorophyll a concentrations. Particulate organic carbon and nitrogen (POC and PON) increased by 40 and 70% respectively from February to April 2014. Dissolved organic carbon (DOC) increased by 70% in December and stayed elevated for at least 4 months, indicating high organic matter release by primary producers. Such strong cascading effects of upwelling on organic matter dynamics on coral reefs have not been reported previously, although likely impacting many reefs in comparable upwelling systems.
ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests

The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the ‘best close match’ test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.
Parental Effect of Long Acclimatization on Thermal Tolerance of Juvenile Sea Cucumber Apostichopus japonicus

To evaluate the thermal resistance of marine invertebrates to elevated temperatures under scenarios of future climate change, it is crucial to understand parental effect of long acclimatization on thermal tolerance of offspring. To test whether there is parental effect of long acclimatization, adult sea cucumbers (Apostichopus japonicus) from the same broodstock were transplanted southward and acclimatized at high temperature in field mesocosms. Four groups of juvenile sea cucumbers whose parents experienced different durations of high temperature acclimatization were established. Upper thermal limits, oxygen consumption and levels of heat shock protein mRNA of juveniles was determined to compare thermal tolerance of individuals from different groups. Juvenile sea cucumbers whose parents experienced high temperature could acquire high thermal resistance. With the increase of parental exposure duration to high temperature, offspring became less sensitive to high temperature, as indicated by higher upper thermal limits (LT50), less seasonal variations of oxygen consumption, and stable oxygen consumption rates between chronic and acute thermal stress. The relatively high levels of constitutive expression of heat-shock proteins should contribute to the high thermal tolerance. Together, these results indicated that the existence of a parental effect of long acclimatization would increase thermal tolerance of juveniles and change the thermal sensitivity of sea cucumber to future climate change.
Relative Pigment Composition and Remote Sensing Reflectance of Caribbean Shallow-Water Corals

Reef corals typically contain a number of pigments, mostly due to their symbiotic relationship with photosynthetic dinoflagellates. These pigments usually vary in presence and concentration and influence the spectral characteristics of corals. We studied the variations in pigment composition among seven Caribbean shallow-water Scleractinian corals by means of High Performance Liquid Chromatography (HPLC) analysis to further resolve the discrimination of corals. We found a total of 27 different pigments among the coral species, including some alteration products of the main pigments. Additionally, pigments typically found in endolithic algae were also identified. A Principal Components Analysis and a Hierarchical Cluster Analysis showed the separation of coral species based on pigment composition. All the corals were collected under the same physical environmental conditions. This suggests that pigment in the coral’s symbionts might be more genetically-determined than influenced by prevailing physical conditions of the reef. We further investigated the use of remote sensing reflectance (Rrs) as a tool for estimating the total pigment concentration of reef corals. Depending on the coral species, the Rrs and the total symbiont pigment concentration per coral tissue area correlation showed 79.5–98.5% confidence levels demonstrating its use as a non-invasive robust technique to estimate pigment concentration in studies of coral reef biodiversity and health.
Point Me in the Right Direction: Same and Cross Category Visual Aftereffects to Directional Cues

Of the many hand gestures that we use in communication pointing is one of the most common and powerful in its role as a visual referent that directs joint attention. While numerous studies have examined the developmental trajectory of pointing production and comprehension, very little consideration has been given to adult visual perception of hand pointing gestures. Across two studies, we use a visual adaptation paradigm to explore the mechanisms underlying the perception of proto-declarative hand pointing. Twenty eight participants judged whether 3D modeled hands pointed, in depth, at or to the left or right of a target (test angles of 0°, 0.75° and 1.5° left and right) before and after adapting to either hands or arrows which pointed 10° to the right or left of the target. After adaptation, the perception of the pointing direction of the test hands shifted with respect to the adapted direction, revealing separate mechanisms for coding right and leftward pointing directions. While there were subtle yet significant differences in the strength of adaptation to hands and arrows, both cues gave rise to a similar pattern of aftereffects. The considerable cross category adaptation found when arrows were used as adapting stimuli and the asymmetry in aftereffects to left and right hands suggests that the adaptation aftereffects are likely driven by simple orientation cues, inherent in the morphological structure of the hand, and not dependent on the biological status of the hand pointing cue. This finding provides evidence in support of a common neural mechanism that processes these directional social cues, a mechanism that may be blind to the biological status of the stimulus category.
The Dynamics of Speed Selection and Psycho-Physiological Load during a Mountain Ultramarathon

Background Exercise intensity during ultramarathons (UM) is expected to be regulated as a result of the development of psycho-physiological strain and in anticipation of perceived difficulties (duration, topography). The aim of this study was to investigate the dynamics of speed, heart rate and perceived exertion during a long trail UM in a mountainous setting. Methods Fifteen participants were recruited from competitors in a 106 km trail mountain UM with a total elevation gain and loss of 5870 m. Speed and gradient, heart rate (HR) and ratings of perceived exertion (dissociated between the general [RPEGEN] and knee extensor fatigue [RPEKE] and collected using a voice recorder) were measured during the UM. Self-selected speed at three gradients (level, negative, positive), HR, RPEGEN and RPEKE were determined for each 10% section of total event duration (TED). Results The participants completed the event in 18.3 ± 3.0 h, for a total calculated distance of 105.6 ± 1.8 km. Speed at all gradients decreased, and HR at all gradients significantly decreased from 10% to 70%, 80% and 90%, but not 100% of TED. RPEGEN and RPEKE increased throughout the event. Speed increased from 90% to 100% of TED at all gradients. Average speed was significantly correlated with total time stopped (r = -.772; p = .001; 95% confidence interval [CI] = -1.15, -0.39) and the magnitude of speed loss (r = .540; p = .038; 95% CI = -1.04, -0.03), but not with the variability of speed (r = -.475; p = .073; 95% CI = -1.00, 0.05). Conclusions Participants in a mountain UM event combined positive pacing strategies (speed decreased until 70–90% of TED), an increased speed in the last 10% of the event, a decrease in HR at 70–90% of TED, and an increase in RPEGEN and RPEKE in the last 30% of the event. A greater speed loss and less total time stopped were the factors associated with increased total performance. These results could be explained by theoretical perspectives of a complex regulatory system modulating motor drive in anticipation of perceived difficulties such as elevation changes.
Structural Implications for the Formation and Function of the Complement Effector Protein iC3b

Complement-mediated opsonization, phagocytosis, and immune stimulation are critical processes in host defense and homeostasis, with the complement activation fragment iC3b playing a key effector role. To date, however, there is no high-resolution structure of iC3b, and some aspects of its structure-activity profile remain controversial. Here, we employed hydrogen–deuterium exchange mass spectrometry to describe the structure and dynamics of iC3b at a peptide resolution level in direct comparison with its parent protein C3b. In our hydrogen–deuterium exchange mass spectrometry study, 264 peptides were analyzed for their deuterium content, providing almost complete sequence coverage for this 173-kDa protein. Several peptides in iC3b showed significantly higher deuterium uptake when compared with C3b, revealing more dynamic, solvent-exposed regions. Most of them resided in the CUB domain, which contains the heptadecapeptide C3f that is liberated during the conversion of C3b to iC3b. Our data suggest a highly disordered CUB, which has acquired a state similar to that of intrinsically disordered proteins, resulting in a predominant form of iC3b that features high structural flexibility. The structure was further validated using an anti-iC3b mAb that was shown to target an epitope in the CUB region. The information obtained in this work allows us to elucidate determinants of iC3b specificity and activity and provide functional insights into the protein’s recognition pattern with respect to regulators and receptors of the complement system.
The Global Land Surface Satellite (GLASS) Remote Sensing Data Processing System and Products

Using remotely sensed satellite products is the most efficient way to monitor global land, water, and forest resource changes, which are believed to be the main factors for understanding global climate change and its impacts. A reliable remotely sensed product should be retrieved quantitatively through models or statistical methods. However, producing global products requires a complex computing system and massive volumes of multi-sensor and multi-temporal remotely sensed data. This manuscript describes the ground Global LAnd Surface Satellite (GLASS) product generation system that can be used to generate long-sequence time series of global land surface data products based on various remotely sensed data. To ensure stabilization and efficiency in running the system, we used the methods of task management, parallelization, and multi I/O channels. An array of GLASS remote sensing products related to global land surface parameters are currently being produced and distributed by the Center for Global Change Data Processing and Analysis at Beijing Normal University in Beijing, China. These products include Leaf Area Index (LAI), land surface albedo, and broadband emissivity (BBE) from the years 1981 to 2010, downward shortwave radiation (DSR) and photosynthetically active radiation (PAR) from the years 2008 to 2010.
GPR68, a proton‐sensing GPCR, mediates interaction of cancer‐associated fibroblasts and cancer cells

The microenvironment of pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense fibrotic stroma (desmoplasia) generated by pancreatic cancer‐associated fibroblasts (CAFs) derived from pancreatic stellate cells (PSCs) and pancreatic fibroblasts (PFs). Using an unbiased GPCRomic array approach, we identified 82 G‐protein‐coupled receptors (GPCRs) commonly expressed by CAFs derived from 5 primary PDAC tumors. Compared with PSCs and PFs, CAFs have increased expression of GPR68 (a proton‐sensing GPCR), with the results confirmed by immunoblotting, The Cancer Genome Atlas data, and immunohistochemistry of PDAC tumors. Coculture of PSCs with PDAC cells, or incubation with TNF‐α, induced GPR68 expression. GPR68 activation (by decreasing the extracellular pH) enhanced IL‐6 expression via a cAMP/PKA/cAMP response element binding protein signaling pathway. Knockdown of GPR68 by short interfering RNA diminished low pH‐induced production of IL‐6 and enhancement of PDAC cell proliferation by CAF conditioned media. CAFs from other gastrointestinal cancers also express GPR68. PDAC cells thus induce expression by CAFs of GPR68, which senses the acidic microenvironment, thereby increasing production of fibrotic markers and IL‐6 and promoting PDAC cell proliferation. CAF‐expressed GPR68 is a mediator of low‐pH‐promoted regulation of the tumor microenvironments, in particular to PDAC cell‐CAF interaction and may be a novel therapeutic target for pancreatic and perhaps other types of cancers. —Wiley, S. Z. , Sriram, K. , Liang, W. , Chang, S. E. , French, R. , McCann, T. , Sicklick, J., Nishihara, H. , Lowy, A. M. , Insel, P. A. GPR68, a proton‐sensing GPCR, mediates interaction of cancer‐associated fibroblasts and cancer cells. FASEB J. 32,1170‐1183 (2018). www.fasebj. org
Neural Sketch Learning for Conditional Program Generation

We study the problem of generating source code in a strongly typed, Java-like programming language, given a label (for example a set of API calls or types) carrying a small amount of information about the code that is desired. The generated programs are expected to respect a "realistic" relationship between programs and labels, as exemplified by a corpus of labeled programs available during training. Two challenges in such conditional program generation are that the generated programs must satisfy a rich set of syntactic and semantic constraints, and that source code contains many low-level features that impede learning. We address these problems by training a neural generator not on code but on program sketches, or models of program syntax that abstract out names and operations that do not generalize across programs. During generation, we infer a posterior distribution over sketches, then concretize samples from this distribution into type-safe programs using combinatorial techniques. We implement our ideas in a system for generating API-heavy Java code, and show that it can often predict the entire body of a method given just a few API calls or data types that appear in the method.
Proactive Cross-Channel Gain Estimation for Spectrum Sharing in Cognitive Radio

In an underlay cognitive radio network, the cross-channel gain from a cognitive transmitter (CT) to a primary receiver (PR) is crucial for spectrum sharing. By exploiting the relaying capability of the CT, we propose a proactive estimation scheme for the cross-channel gain. Specifically, the CT proactively acts as a full-duplex amplify-and-forward (AF) relay for primary transceivers to trigger the power adaption of a primary transmitter (PT). By carefully designing the relay signal, the CT is able to obtain an estimation of the cross-channel gain by observing the power adaption. To demonstrate the accuracy of the estimation, we analytically characterize both an upper bound and a lower bound of the estimation performance. Furthermore, we study the impact of CT's relaying on the primary transmission and observe that the impact is related to the CT's location. By introducing a factor φ (0 ≤ φ ≤ 1) to denote the probability that the CT's relaying improves the primary transmission instead of causes interference, we design the CT location as a function of φ. Numerical results show that the estimation error of the proactive estimation scheme can be as small as 1.7% with success estimation probability around 91%. By comparing with the state of the art, we show the advantages of the proposed estimator.
The Different Association between Serum Ferritin and Mortality in Hemodialysis and Peritoneal Dialysis Patients Using Japanese Nationwide Dialysis Registry

Background/Aims Monitoring of serum ferritin levels is widely recommended in the management of anemia among patients on dialysis. However, associations between serum ferritin and mortality are unclear and there have been no investigations among patients undergoing peritoneal dialysis (PD). Methods Baseline data of 191,902 patients on dialysis (age, 65 ± 13 years; male, 61.1%; median dialysis duration, 62 months) were extracted from a nationwide dialysis registry in Japan at the end of 2007. Outcomes, such as one-year mortality, were then evaluated using the registry at the end of 2008. Results Within one year, a total of 15,284 (8.0%) patients had died, including 6,210 (3.2%) cardiovascular and 2,707 (1.4%) infection-related causes. Higher baseline serum ferritin levels were associated with higher mortality rates among patients undergoing hemodialysis (HD). In contrast, there were no clear associations between serum ferritin levels and mortality among PD patients. Multivariate Cox regression analysis of HD patients showed that those in the highest serum ferritin decile group had higher rates of all-cause and cardiovascular mortality than those in the lowest decile group (hazard ratio [HR], 1.54; 95% confidence interval [CI], 1.31–1.81 and HR, 1.44; 95% CI, 1.13–1.84, respectively), whereas associations with infection-related mortality became non-significant (HR, 1.14; 95% CI, 0.79–1.65). Conclusions Using Japanese nationwide dialysis registry, higher serum ferritin values were associated with mortality not in PD patients but in HD patients.
Enhancement of Treatment Efficiency of Recalcitrant Wastewater Containing Textile Dyes Using a Newly Developed Iron Zeolite Socony Mobil-5 Heterogeneous Catalyst

Fenton oxidation, an advanced oxidation process, is an efficient method for the treatment of recalcitrant wastewaters. Unfortunately, it utilizes H2O2 and iron-based homogeneous catalysts, which lead to the formation of high volumes of sludge and secondary pollutants. To overcome these problems, an alternate option is the usage of heterogeneous catalyst. In this study, a heterogeneous catalyst was developed to provide an alternative solution for homogeneous Fenton oxidation. Iron Zeolite Socony Mobile-5 (Fe-ZSM-5) was synthesized using a new two-step process. Next, the catalyst was characterized by scanning electron microscopy, energy-dispersive X-ray spectroscopy, fourier transform infrared spectroscopy, and Brunauer-Emmett-Teller analysis and tested against a model wastewater containing the azo dye Acid Blue 113. Results showed that the loading of iron particles reduced the surface area of the catalyst from 293.59 to 243.93 m2/g; meanwhile, the average particle size of the loaded material was 12.29 nm. Furthermore, efficiency of the developed catalyst was evaluated by performing heterogeneous Fenton oxidation. Taguchi method was coupled with principal component analysis in order to assess and optimize mineralization efficiency. Experimental results showed that under optimized conditions, over 99.7% degradation and 77% mineralization was obtained, with a 90% reduction in the consumption of the developed catalyst. Furthermore, the developed catalyst was stable and reusable, with less than 2% leaching observed under optimized conditions. Thus, the present study proved that newly developed catalyst has enhanced the oxidation process and reduced the chemicals consumption.