bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrothermal vein distribution in skarn type alteration zone of area X at PT. Freeport Indonesia
Authors: Tobing E. , Sihombing F M H 
Published: October 2021

Abstract
Kucing Liar is an economic skarn altered deposited located in Tembagapura, Papua. This deposit was found on Late Cretaceous to Miocene sedimentary rocks of Kembelangan Group and Papua New Guinea Limestone Group. The alteration from this deposit can be divided into groundmass alteration, named penetrative alteration, and selvage alteration forming hydrothermal veins. The penetrative alteration is divided into 9 zones, meanwhile the hydrothermal veins are classified by its mineral composition into 5 types of anhydrite veins, calcite, quartz, sulphide, and gypsum veins. Each vein type will associate the most with different penetrative alteration zone due to its protolith composition and on what stage the vein formed. The anhydrite and quartz veins are found to be associated the most with calc-silicate hornfels zone with the anhydrite sources came from calcite and quartz sources came from the surrounding rocks which the alteration fluid passed through. The sulphide and calcite veins are found to associate the most with dolomitization zone with calcite sources came from the surrounding rock and sulphide deposited filling the open spaces, such as fracture, in crystalline dolostone. Gypsum veins are found to associate the most with fault zone because it formed from the alteration of calcite by faulting process.
Study of altered lithologies in Gunung Lawu, Central Java, Indonesia using petrographic analysis
Authors: Sari E K , Ponka M A , Sahradani D N , Yoga D A , Supriyanto  
Published: October 2021

Abstract
Gunung Lawu is one of the areas that have geothermal potential in Indonesia. One way to find out if an area has a geothermal potential is to know the alteration that occurs in the rocks in that area. Alteration is a very complicated process that involves changes in mineralogy, chemistry, and texture caused by the interaction of hot fluids with the rock in its path. This research aims to identify mineral and intensity of alteration in the research area with petrographic analysis and hand specimen description. The petrographic analysis method is used to identify unaltered or altered minerals present in the sample rocks of the study area. In addition to using petrographic analysis, it is also seen through hand specimen descriptions and also outcrops to see the lithology of rocks in the research area. From the sample of this research, it can be classified by three categories. There are unaltered rocks, weak intensity alteration and strong intensity alteration. Unaltered rocks were found in SLM and BNA, weak intensity alteration was found in NGY 1 and strong intensity alteration was found in LWU. In NGY 1 sample, chlorite alteration mineral was found, while in LWU, goethite alteration mineral was found. The occurrence of alteration in the area may be due to the area being passed by faults which interact with hydrothermal fluid. These faults also become the fluid pathway for the geothermal reservoir. The heat from the reservoir is able to change the mineral composition of the rock. In LWU, a fault is passed which produces fumarole manifestations, and NGY 1 is passed by a fault that forms hot spring manifestations.
Spatial pattern change of land use change in tidal flood area of the coast of Cirebon Regency
Authors: Andika I P A , Tambunan M P , Marko K 
Published: October 2021

Abstract
Tidal flood is one of the threats found in the coastal areas of Cirebon Regency, especially in Pangenan, Gebang and Losari Districts. The changing coastal conditions and the changing land use have worsened the tidal flood. The purpose of this research is to analyse the spatial pattern of land use change in the tidal flood area. This study uses spatial analysis and temporal and spatial metrics. Temporal, spatial analysis is used to see changes in land use in tidal flood areas in 2002, 2009, and 2019, while spatial metrics are used to see these patterns, especially aggregation and diversity. The results of processing show that changes in land use in 2002–2019 were dominated by ponds and irrigated rice fields. The largest land use area in the tidal flood area is in ponds, but the increase has continued to occur in residential and built-up land from 2002 to 2019. Overall, the spatial metric results show that land use fragmentation in the coastal zone of Cirebon Regency in the tidal flood area is increasing. However, the development of land use in the coastal district of Cirebon Regency is low due to tidal flood.
Lobster aquaculture location selection based on oceanographic conditions using remote sensing (Case study: Ciletuh Bay, Sukabumi, Indonesia)
Authors: Suhermat M , Dimyati M , Supriatna  , Martono  , Susanti I 
Published: October 2021

Abstract
Lobster (Panulirus spp.) is one of the marine resources that has high economic value, both locally and internationally. Ciletuh Bay has potential as a lobster cultivation location. The growth of lobsters is influenced by the conditions of the aquatic environment, especially the salinity and sea surface temperature. Remote sensing method can identify and analyse salinity and sea surface temperature. Salinity value obtained using Cilamaya algorithm, and sea surface temperature obtained using Syariz algorithm. This study aims to select a suitable location for lobster cultivation in Ciletuh Bay using a remote sensing approach. Map of salinity distribution and sea surface temperature is obtained from Landsat-8 imagery. The condition of water quality parameters in the Ciletuh Bay was quite suitable to be used as a lobster cultivation location. The distribution of salinity shows a dominance value 28.0–32.0, the distribution of sea surface temperature shows a dominance value 25.0–29.0, and the distribution of pH shows a dominance value 7.0–14.0. Based on the analysis of sea water quality parameters in Ciletuh Bay, most of the waters of Ciletuh Bay have a high suitability for lobster cultivation, covering an area of 253.01 ha.
Optimizing genomic control in mixed model associations with binary diseases
Authors: Song Yuxin , Yang Li’ang , Jiang Li , Hao Zhiyu , Yang Runqing , Xu Pao 
Published: October 2021

Abstract
Complex computation and approximate solution hinder the application of generalized linear mixed models (GLMM) into genome-wide association studies. We extended GRAMMAR to handle binary diseases by considering genomic breeding values (GBVs) estimated in advance as a known predictor in genomic logit regression, and then reduced polygenic effects by regulating downward genomic heritability to control false negative errors produced in the association tests. Using simulations and case analyses, we showed in optimizing GRAMMAR, polygenic effects and genomic controls could be evaluated using the fewer sampling markers, which extremely simplified GLMM-based association analysis in large-scale data. Further, joint association analysis for quantitative trait nucleotide (QTN) candidates chosen by multiple testing offered significant improved statistical power to detect QTNs over existing methods.
Molecular ecology of the fiddler crab Austruca perplexa (H. Milne Edwards, 1852): genetic divergence along a major biogeographical barrier, Wallace’s Line
Authors: Hardianto Eko , Permata Wijayanti Diah , Shy Jhy-Yun , Mather Peter , Hughes Jane , Imai Hideyuki 
Published: October 2021

Abstract
Genetic diversity and population structure in the fiddler crab Austruca perplexa were investigated to acquire a better understanding of the evolutionary history of the species. Nucleotide sequence analysis was performed from a polymerase chain reaction-amplified fragment of the mitochondrial DNA control region. A 691 bp nucleotide sequence was obtained from 618 specimens collected from 13 sites across Japan, Taiwan, the Philippines, Indonesia and Australia. Haplotype diversity ranged from 0.8 to 0.99, and nucleotide diversity values were lower (range, 0.30–1.9%) than those reported previously for other crustacean taxa. Gene flow was evident within populations in Japan and western Indonesia, but absent among all other populations, including eastern Indonesia. This pattern conforms to the one observed in many other marine taxa across the major biogeographical region referred to as Wallacea. The population pairwise fixation index (FST) and FSTP-values were high and significant among many sites, implying that gene flow is restricted among most of the geographical regions sampled here. We hypothesize that physical oceanic barriers coupled with a short pelagic larval duration are responsible for creating the patterns we found. Strong evidence for population structure in a species that has relatively high dispersal potential, resulting in among-population differentiation, is a potential driver of evolutionary novelty. Our results provide a foundation for developing better conservation strategies for this widespread intertidal species.
Nuclear–plastid discordance indicates past introgression inEpidendrumspecies (Laeliinae: Orchidaceae) with highly variable chromosome numbers
Authors: Pessoa Edlley M , Nollet Felipe , Magalhães Rafael F , Viruel Juan , Pinheiro Fábio , Chase Mark W 
Published: October 2021

AbstractHere we study a challenging group of karyotypically highly variable Epidendrum spp. using phylogenetic methods to help understand how hybridization/introgression contributes to karyotype evolution. We hypothesize that species with great chromosome number variation are a result of past hybridization/introgression. Conflicting topologies in trees constructed using separate plastid and nuclear datasets suggest past hybridization events that occurred most probably at least 3.7 Mya. A basic number x = 14 and substantial karyotype change followed by species divergence are suggested. Descending dysploidy and polyploidy were the most frequent changes estimated across the phylogenetic tree of the group. Two species, Epidendrum secundum and E. xanthinum, have probably experienced unidirectional gene flow involving their ancestors (the pollen recipients) and ancestors of E. puniceoluteum and E. denticulatum/E. flammeum, respectively, the pollen donors. However, it is not possible to say whether hybridization participated in the origin of E. secundum and E. xanthinum or merely contributed to their genomic divergence and karyotype change through introgression as has been observed in modern hybrid zones in Epidendrum. This pattern of introgression causing karyotype disruption and divergence could help explain the enigma of some highly diverse genera, such as Epidendrum. Further studies using a wider sampling of the genus could test if gene flow and karyotype variability are associated with the increase of speciation rates.
Atypical development of Broca’s area in a large family with inherited stuttering
Authors: Thompson-Lake Daisy G Y , Scerri Thomas S , Block Susan , Turner Samantha J , Reilly Sheena , Kefalianos Elaina , Bonthrone Alexandra F , Helbig Ingo , Bahlo Melanie , Scheffer Ingrid E , Hildebrand Michael S , Liégeois Frédérique J , Morgan Angela T 
Published: October 2021

Abstract
Developmental stuttering is a condition of speech dysfluency, characterized by pauses, blocks, prolongations and sound or syllable repetitions. It affects around 1% of the population, with potential detrimental effects on mental health and long-term employment. Accumulating evidence points to a genetic aetiology, yet gene–brain associations remain poorly understood due to a lack of MRI studies in affected families. Here we report the first neuroimaging study of developmental stuttering in a family with autosomal dominant inheritance of persistent stuttering.
We studied a four-generation family, 16 family members were included in genotyping analysis. T1-weighted and diffusion-weighted MRI scans were conducted on seven family members (six male; aged 9–63 years) with two age and sex matched controls without stuttering (n = 14). Using Freesurfer, we analysed cortical morphology (cortical thickness, surface area and local gyrification index) and basal ganglia volumes. White matter integrity in key speech and language tracts (i.e. frontal aslant tract and arcuate fasciculus) was also analysed using MRtrix and probabilistic tractography.
We identified a significant age by group interaction effect for cortical thickness in the left hemisphere pars opercularis (Broca’s area). In affected family members this region failed to follow the typical trajectory of age-related thinning observed in controls. Surface area analysis revealed the middle frontal gyrus region was reduced bilaterally in the family (all cortical morphometry significance levels set at a vertex-wise threshold of P &lt; 0.01, corrected for multiple comparisons). Both the left and right globus pallidus were larger in the family than in the control group (left P = 0.017; right P = 0.037), and a larger right globus pallidus was associated with more severe stuttering (rho = 0.86, P = 0.01). No white matter differences were identified. Genotyping identified novel loci on chromosomes 1 and 4 that map with the stuttering phenotype.
Our findings denote disruption within the cortico-basal ganglia-thalamo-cortical network. The lack of typical development of these structures reflects the anatomical basis of the abnormal inhibitory control network between Broca’s area and the striatum underpinning stuttering in these individuals. This is the first evidence of a neural phenotype in a family with an autosomal dominantly inherited stuttering.
Neuronal Electrical Ongoing Activity as Cortical Areas Signature: An Insight from MNI Intracerebral Recording Atlas
Authors: Armonaite Karolina , Bertoli Massimo , Paulon Luca , Gianni Eugenia , Balsi Marco , Conti Livio , Tecchio Franca 
Published: October 2021

Abstract
The time course of the neuronal activity in the brain network, the neurodynamics, reflects the structure and functionality of the generating neuronal pools. Here, using the intracranial stereo-electroencephalographic (sEEG) recordings of the public Montreal Neurological Institute (MNI) atlas, we investigated the neurodynamics of primary motor (M1), somatosensory (S1) and auditory (A1) cortices measuring power spectral densities (PSD) and Higuchi fractal dimension (HFD) in the same subject (M1 vs. S1 in 16 subjects, M1 vs. A1 in 9, S1 vs. A1 in 6).
We observed specific spectral features in M1, which prevailed above beta band, S1 in the alpha band, and A1 in the delta band. M1 HFD was higher than S1, both higher than A1.
A clear distinction of neurodynamics properties of specific primary cortices supports the efforts in cortical parceling based on this expression of the local cytoarchitecture and connectivity. In this perspective, we selected within the MNI intracortical database a first set of primary motor, somatosensory and auditory cortices’ representatives to query in recognizing ongoing patterns of neuronal communication.
Potential clinical impact stands primarily in exploiting such exchange patterns to enhance the efficacy of neuromodulation intervention to cure symptoms secondary to neuronal activity unbalances.
Choices in hemodialysis therapies: variants, personalized therapy and application of evidence-based medicine
Authors: Canaud Bernard , Stuard Stefano , Laukhuf Frank , Yan Grace , Canabal Maria Ines Gomez , Lim Paik Seong , Kraus Michael A 
Published: October 2021

ABSTRACTThe extent of removal of the uremic toxins in hemodialysis (HD) therapies depends primarily on the dialysis membrane characteristics and the solute transport mechanisms involved. While designation of ‘flux’ of membranes as well toxicity of compounds that need to be targeted for removal remain unresolved issues, the relative role, efficiency and utilization of solute removal principles to optimize HD treatment are better delineated. Through the combination and intensity of diffusive and convective removal forces, levels of concentrations of a broad spectrum of uremic toxins can be lowered significantly and successfully. Extended clinical experience as well as data from several clinical trials attest to the benefits of convection-based HD treatment modalities. However, the mode of delivery of HD can further enhance the effectiveness of therapies. Other than treatment time, frequency and location that offer clinical benefits and increase patient well-being, treatment- and patient-specific criteria may be tailored for the therapy delivered: electrolytic composition, dialysate buffer and concentration and choice of anticoagulating agent are crucial for dialysis tolerance and efficacy. Evidence-based medicine (EBM) relies on three tenets, i.e. clinical expertise (i.e. doctor), patient-centered values (i.e. patient) and relevant scientific evidence (i.e. science), that have deviated from their initial aim and summarized to scientific evidence, leading to tyranny of randomized controlled trials. One must recognize that practice patterns as shown by Dialysis Outcomes and Practice Patterns Study and personalization of HD care are the main driving force for improving outcomes. Based on a combination of the three pillars of EBM, and particularly on bedside patient–clinician interaction, we summarize what we have learned over the last 6 decades in terms of best practices to improve outcomes in HD patients. Management of initiation of dialysis, vascular access, preservation of kidney function, selection of biocompatible dialysers and use of dialysis fluids of high microbiological purity to restrict inflammation are just some of the approaches where clinical experience is vital in the absence of definitive scientific evidence. Further, HD adequacy needs to be considered as a broad and multitarget approach covering not just the dose of dialysis provided, but meeting individual patient needs (e.g. fluid volume, acid–base, blood pressure, bone disease metabolism control) through regular assessment—and adjustment—of a series of indicators of treatment efficiency. Finally, in whichever way new technologies (i.e. artificial intelligence, connected health) are embraced in the future to improve the delivery of dialysis, the human dimension of the patient–doctor interaction is irreplaceable. Kidney medicine should remain ‘an art’ and will never be just ‘a science’.
Multiplexed Assay to Quantify the PP-Fold Family of Peptides in Human Plasma Using Microflow Liquid Chromatography–Tandem Mass Spectrometry
Authors: Reverter-Branchat Gemma , Eugster Philippe J , Kuenzli Christina , Rindlisbacher Barbara , Stauffer Thomas , Nakas Christos T , Herzig David , Grouzmann Eric , Bally Lia 
Published: October 2021

Abstract

Background
Peptide Tyr-Tyr (PYY1-36), pancreatic polypeptide (PP1-36) and neuropeptide Y (NPY1-36) constitute the PP-fold family of peptides that is involved in metabolic regulation. Very low plasma concentrations and cleavage into active 3–36 fragments challenge bioanalytical assays used for the quantification of these peptides.

Methods
We developed a multiplexed isotopic dilution assay to quantify PYY1-36, PP1-36, and NPY1-36 and their dipeptidyl peptidase-4 (DPP4)-derived metabolites PYY3-36, PP3-36 and NPY3-36. All peptides were immunocaptured from plasma using a monoclonal antibody and quantified by micro-ultra-HPLC-MS/MS. Blood samples from healthy volunteers were collected fasting and 30 min after nutrient stimulation. Method comparison was performed with commercial immunoassays.

Results
Linearity was shown in the measured intervals (r2 &gt; 0.99). The lower limit of quantification (LLOQ) with a CV at 20% was 1.5 pM for PYY1-36 and PYY3-36, 3.0 pM for PP1-36 and PP3-36, 0.8 pM for NPY1-36 and 0.5 pM for NPY3-36. In all cases, intra- and inter-assay bias and imprecision were &lt;21%. Pre-analytical stability required addition of a protease inhibitor cocktail. Physiological concentrations of PYY3-36, NPY3-36, PP1-36 and PP3-36 were above the LLOQ in 43% to 100% of the samples. PYY1-36 and NPY1-36 were above the LLOQ in 9% and 0% of the samples, respectively. Immunoassays showed higher concentrations of measurands and poor agreement when compared with micro-UHPLC-MS/MS.

Conclusions
The assay allowed for specific multiplexed analysis of the PP-fold family of peptides and their DPP4-cleaved fragments in a single sample, thereby offering new perspectives to study the role and therapeutic potential of these essential peptide hormones in health and metabolic disease.
Phenotyping patients with borderline elevated esophageal acid exposure
Authors: Reddy Chanakyaram A , Wenzke Kevin , Watts Lydia S , Armstrong Moira , Chen Vincent L , Baker Jason R , Chen Joan W 
Published: October 2021

Summary
Acid exposure time (AET) &lt;4% on ambulatory reflux monitoring definitively rules out pathologic gastroesophageal acid reflux, while AET &gt;6% indicates pathologic reflux per the Lyon Consensus, leaving AET of 4–6% as borderline. We aimed to elucidate the borderline AET population and identify metrics that could help differentiate this group. A total of 50 subjects in each group, AET &lt;4, 4–6, and &gt;6% on pH-impedance monitoring between 2015 and 2019, were retrospectively reviewed. In addition to demographic and clinical information, the extracted data included mean nocturnal baseline impedance (MNBI) on reflux study and high-resolution manometry (HRM) parameters and diagnosis. After excluding patients with prior foregut surgery, major esophageal motility disorder, or unreliable impedance testing, a total of 89 subjects were included in the analysis (25 with normal AET &lt; 4%, 38 with borderline 4–6%, 26 with abnormal &gt;6%). MNBI in borderline AET patients was significantly lower compared to normal AET (1607.7 vs. 2524.0 ohms, P &lt; 0.01), and higher than abnormal AET (951.5 ohms, P &lt; 0.01). Borderline subjects had a greater frequency of ineffective esophageal motility (IEM) diagnosis per Chicago classification v3.0 (42.1 vs. 8.0%, P = 0.01), but did not demonstrate any differences compared to abnormal subjects (34.6%, P = 0.56). Patients with borderline AET had an average MNBI that was in between normal AET and abnormal AET. Borderline AET patients also commonly demonstrate IEM on HRM, similar to those with abnormal AET. Our findings can be potentially useful in assigning higher clinical significance for patients found to have borderline AET with concomitant low MNBI and IEM on manometry.
A case report of ventricular septal defect complicating transcatheter aortic valve implant for aortic regurgitation: novel complication and technical considerations
Authors: Hartnett Jack , Brandon Lisa , Waterhouse Deirdre , Murphy Ross T , Walsh Kevin P , Spence Mark S , Maree Andrew O 
Published: October 2021

Abstract

Background
Transcatheter aortic valve implantation (TAVI) has proven efficacy in the treatment of aortic stenosis (AS). Understandably, there is increasing enthusiasm for its use to treat aortic regurgitation (AR). However, there are significant anatomical differences between AS and AR which make TAVI for AR more complex.

Case summary
We present the case of technically challenging TAVI for severe AR, which was complicated by a traumatic ventricular septal defect (VSD) that required percutaneous closure. To our knowledge, this is the first published case of VSD post-TAVI for AR.

Discussion
This unanticipated complication highlights anatomical differences between TAVI use in AS and AR. Lack of aortic valve calcification and excessive annular compliance made stable deployment of a self-expanding valve extremely challenging. Despite device oversizing, repeated embolization of the prosthesis into the left ventricular outflow tract traumatized the interventricular septum.