bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifikasi Jenis -Jenis Mangrove di Kawasan Hutan Mangrove Desa Maidi Kecamatan Oba Selatan
Authors: Husen Sriayu I. , Hikmah Nur , Nurdin Aqshan Sadikin 
Published: June 2024

Mangrove yang berada di Desa Maidi Kecamatan Oba Selatan memiliki berbagai macam ekosistem yang menyebabkan keragaman jenis tumbuhan. Tujuan dari penelitian ini adalah untuk mengetahui jenis mangrove apa saja yang terdapat di kawasan hutan mangrove Desa Maidi Kecamatan Oba Selatan dan bagaimana keanekaragaman jenis mangrove di kawasan hutan mangrove Desa Maidi Kecamatan Oba Selatan. Metode yang digunakan yaitu metode kualitatif yang bertujuan untuk menjelaskan suatu fenomena mendalam dan dilakukan dengan pengumpulan data sedalam-dalamnya. Berdasarkan hasil penelitian identifikasi jenis mangrove di kawasan hutan mangrove Desa Maidi Kecamatan Oba Selatan, terdapat 3 jenis mangrove yang ditemukan dan memiliki tingkat keragaman lebih sedikit atau rendah. Jenis-jenis Mangrove yang berada di lokasi penelitian yaitu: Avicennia Alba, Rhizophora Apiculata, dan Avecennia Lanata. Keanekagaman jenis (H’) mangrove di kawasan hutan mangrove Desa Maidi Kecamatan Oba Selatan sebesar 0,58591 yang menunjukan tingkat keanakaragaman yang sedikit atau rendah.
Kata kunci: Desa Maidi, Keanekaragaman jenis, Mangrove.
REPLEACEMENT MESIN FRAIS WMD-25VL PENGGERAK KONVENSIONAL MENJADI PENGGERAK OTOMATIS MENGGUNAKAN MOTOR STEPPER NEMA 23 3A DAN LIMIT SWITCH ME-8108
Authors: AHFANDI ACHMAD , Basuki  , Fajar Satriya Hadi  , Mochamad Arif Irfa’i  
Published: June 2024

Dudukan motor stepper memiliki 3 axis yaitu axis X, axis Y dan axis Z. Desain yang digunakan untuk membuat dudukan menggunakan Autodesk Inventor 2017. Setiap dudukan memilki ukuran yang berbeda. Axis X panjang 179mm, lebar 77,5mm dan tebal 10mm. Axis Y panjang 118mm, lebar 58 mm dan tebal 10mm. Axis Z panjang 150mm, lebar 100mm dan tebal 10mm. Kinerja limit switch ME-8108 sama seperti pada saklar lampu ON/OFF yaitu hanya akan terhubung pada saat katupnya ditekan dan akan terputus saat katup tidak ditekan. Pada saat axis bergerak dan saat sumbu axis melewati garis yang ditentukan, maka saklar akan menekan dan axis akan otomatis berhenti. Pengembangan mesin ini menggunakan R&D (research and development). Mencari sumber dari studi literatur, membuat desain mesin frais CNC WMD-25VL,desain dudukan motor stepper, merakit motor stepper yang dihubungkan pada axis dan merakit limit switch yang dihubungkan pada axis. Hasil pengembangan mesin frais WMD-25VL ini telah bekerja dengan baik sesuai dengan fungsinya. Untuk uji fungsional hasil validasi telah di uji oleh tim validator mendapatkan 95%. Uji kelayakan hasil validasi telah di uji oleh tim validator mendapatkan 95%. Hasil rubrik alat kendali pengembangan alat mesin frais CNC WMD-25VL bahwa mesin ini dikategorikan sangat baik.
PENGARUH SPINDLE SPEED DAN FEED RATE TERHADAP KEKASARAN PERMUKAAN AL 6061
Authors: Ahmad Chandra Aditiya  , Mochamad Arif Irfa’I  , Fajar Satriya Hadi  , Basuki  
Published: June 2024

Kemajuan ilmu pengetahuan dan teknologi terjadi dengan sangat cepat, sehingga menjadi lebih kontemporer dan kompleks. Akhirnya, kita membutuhkan mesin yang mampu memproduksi barang dengan kualitas setinggi mungkin. Salah satu solusi dari permasalahan tersebut adalah pemanfaatan mesin CNC (Computer Numerically Controlled).Mesin yang dikontrol secara numerik komputer ini memiliki tingkat ketelitian dan ketelitian dimensi yang tinggi, serta waktu produksi yang lebih cepat, lebih efisien, dan tingkat produktivitas keseluruhan yang tinggi. Penelitian ini dilakukan pada benda kerja jenis Alumunium 6061 dan variasi spindle dan feeding yang dilakukan di Mesin Milling Richon Tipe XK-7132A untuk mengetahui hasil kekasaran permukaan yang dihasilkan. Spindle speed yang diberikan dengan variasi 3500 Rpm; 4000 Rpm; dan 4500 Rpm dan feed rate yang digunakan ialah dengan variasi kecepatan 200 mm/min dan 300 mm/min serta. Pengujian pada setiap specimen menggunakan alat Surface roughness Tester dan dilakukan pada seluruh specimen, penelitian ini menggunakan proses eksperimen dengan pemaparan hasil penelitian menggunakan metode deskriptif kuantitatif. Hasil dari penelitian ini yaitu tingkat kekasaran permukaan tertinggi ter pada variasi spindle speed 3500 Rpm menggunakan feed rate 300 mm/min yang menghasilkan Ra sebesar 0,86 µm. Sedangkan hasil kekasaran terendah didapat pada variasi spindle speed 4500 Rpm dan feed rate 300 mm/min dengan nilai kekasaran yang dihasilkan 0,37 µm. Diketahui bahwa pada spindle speed 4500 Rpm akan menghasilkan kekasaran terendah pada feed rate 200 mm/min . Namun pada penggunaan spindle speed 4500 Rpm akan didapat kekasaran terbaik pada feed rate terbesar yaitu 300 mm/min. Sehingga disimpulkan bahwa terjadi pengaruh pada setiap penggunaan variasi spindle speed dan feed rate terhadap hasil kekasaran permukaan.
Postprandial glycemic response to a high-protein diabetes-specific nutritional shake compared to isocaloric instant oatmeal in people with type 2 diabetes: a randomized, controlled, crossover trial
Authors: Thomas Sara , Besecker Beth , Choe Yong , Christofides Elena 
Published: June 2024

IntroductionMinimizing postprandial glucose response is an important goal for overall diabetes management. Diabetes-specific nutritional shakes (DSNS) have been clinically shown to minimize postprandial glucose response in people with type 2 diabetes (T2DM) compared to high-glycemic foods. However, it is unknown how a high-protein, low-fat DSNS impacts the GLP-1 response.MethodsWe tested the postprandial glucose, insulin, and GLP-1 response to a high-protein, low-fat diabetes-specific nutritional shake (DSNS-HP) compared to isocaloric instant oatmeal (IOM) in a randomized, controlled, crossover study in adults with T2DM (n = 24). Participants were randomly selected to receive IOM or DSNS-HP on two test days. Glucose, insulin, and total GLP-1 concentration were measured at baseline and 15, 30, 45, 60, 90, 120, 180, and 240 min postprandially.ResultsCompared to IOM, the glucose-positive area under the curve (pAUC) was significantly lower (P = .021). DSNS-HP significantly increased GLP-1 pAUC response by 213% (P &lt;.001) with a corresponding increase in insulin pAUC (P = .033) compared to IOM.DiscussionA high-protein, low-fat DSNS leads to favorable changes in GLP-1 response and is a suitable option to minimize blood glucose response in people with type 2 diabetes.
Ceftazidime/avibactam resistance is associated with PER-3-producing ST309 lineage in Chilean clinical isolates of non-carbapenemase producing Pseudomonas aeruginosa
Authors: Soto Katherine D. , Alcalde-Rico Manuel , Ugalde Juan A. , Olivares-Pacheco Jorge , Quiroz Valeria , Brito Bárbara , Rivas Lina M. , Munita José M. , García Patricia C. , Wozniak Aniela 
Published: June 2024

IntroductionCeftazidime/avibactam (CZA) is indicated against multidrug-resistant Pseudomonas aeruginosa, particularly those that are carbapenem resistant. CZA resistance in P. aeruginosa producing PER, a class A extended-spectrum β-lactamase, has been well documented in vitro. However, data regarding clinical isolates are scarce. Our aim was to analyze the contribution of PER to CZA resistance in non-carbapenemase-producing P. aeruginosa clinical isolates that were ceftazidime and/or carbapenem non-susceptible.MethodsAntimicrobial susceptibility was determined through agar dilution and broth microdilution, while blaPER gene was screened through PCR. All PER-positive isolates and five PER-negative isolates were analyzed through Whole Genome Sequencing. The mutational resistome associated to CZA resistance was determined through sequence analysis of genes coding for PBPs 1b, 3 and 4, MexAB-OprM regulators MexZ, MexR, NalC and NalD, AmpC regulators AmpD and AmpR, and OprD porin. Loss of blaPER-3 gene was induced in a PER-positive isolate by successive passages at 43°C without antibiotics. ResultsTwenty-six of 287 isolates studied (9.1%) were CZA-resistant. Thirteen of 26 CZA-resistant isolates (50%) carried blaPER. One isolate carried blaPER but was CZA-susceptible. PER-producing isolates had significantly higher MICs for CZA, amikacin, gentamicin, ceftazidime, meropenem and ciprofloxacin than non-PER-producing isolates. All PER-producing isolates were ST309 and their blaPER-3 gene was associated to ISCR1, an insertion sequence known to mobilize adjacent DNA. PER-negative isolates were classified as ST41, ST235 (two isolates), ST395 and ST253. PER-negative isolates carried genes for narrow-spectrum β-lactamases and the mutational resistome showed that all isolates had one major alteration in at least one of the genes analyzed. Loss of blaPER-3 gene restored susceptibility to CZA, ceftolozane/tazobactam and other β-lactamsin the in vitro evolved isolate. DiscussionPER-3-producing ST309 P. aeruginosa is a successful multidrug-resistant clone with blaPER-3 gene implicated in resistance to CZA and other β-lactams.
Comparison of “Huaxi-1” or “histidine-tryptophan-ketoglutarate” cardioplegia in an animal model
Authors: Yu Xiang , Xiong Wen , Zhang Jie , Lin Jing , Wang Bo , Huang Hong , Du Lei , Xiong Jiyue 
Published: June 2024

BackgroundUsing a pig model of cardiopulmonary bypass, we compared outcomes after cardioplegia either with our in-house “Huaxi-1” solution containing natural blood and crystalloid or with the entirely crystalloid, commercially available “histidine-tryptophan-ketoglutarate” solution.MethodsCardiopulmonary bypass was established in 13 healthy male pigs. Twelve of those animals were randomized to receive a single dose of either Huaxi-1 or entirely crystalloid cardioplegia, while the remaining animal was assigned to receive Huaxi-1 without randomization. All animals were then subjected to whole-heart ischemia for 90 min, followed by 2 h of reperfusion, after which myocardial injury was assessed in terms of cardiac function, myocardial pathology and levels of biomarkers in plasma, while levels of high-energy phosphate in myocardium were assayed using liquid chromatography.ResultsAnimals given Huaxi-1 cardioplegia required significantly less time to be weaned off bypass, they received significantly lower doses of norepinephrine, and they showed significantly higher levels (mean ± SD) of adenosine triphosphate (14 ± 4 vs. 8 ± 2 µg/mg, P = 0.005), adenosine diphosphate (16 ± 2 vs. 13 ± 2 µg/mg, P = 0.046), and total adenine nucleotide (37 ± 4 vs. 30 ± 3 µg/mg, P = 0.006) in myocardium after 2 h of reperfusion. They also showed less severe bleeding, edema and injury to mitochondria and myofibers in myocardium. The two groups did not differ significantly in doses of inotropic drugs received, cardiac output or levels of biomarkers in plasma.ConclusionsIn this animal model of healthy hearts subjected to 90 min of ischemia, Huaxi-1 cardioplegia may be superior to entirely crystalloid cardioplegia for promoting energy generation and attenuating ischemia/reperfusion injury in myocardium.
SpheroMold: modernizing the hanging drop method for spheroid culture
Authors: Guimaraes Ana Paula Pereira , Calori Italo Rodrigo , Bi Hong , Tedesco Antonio Claudio 
Published: June 2024

The hanging drop method is a cost-effective approach for 3D spheroid culture. However, obtaining numerous spheroids in a limited area becomes challenging due to the risk of droplet coalescence, primarly during Petri dish handling. In this study, we describe a general method to fabricate a 3D printing-based support called SpheroMold that facilitates Petri dish handling and enhances spheroid production per unit area. As a proof-of-concept, we designed a digital negative mold which comprised 37 pegs within a 13.52 cm2 area, and then printed it using stereolithography; the density of pegs can be adjusted according to user requirements. The SpheroMold was created by pouring the base and curing agent (10:1) (Sylgard® 184 silicone) into the mold, curing it at 80°C, and then attaching it to the lid of a Petri dish. Our SpheroMold effectively prevented droplet coalescence during Petri dish inversion, enabling the production of numerous 3D spheroids while simplifying manipulation. Unlike conventional techniques, our design also facilitated a larger volume of culture medium per drop compared to a standard Petri dish, potentially decreasing the necessity for frequent medium exchange to sustain cellular health and reducing labor intensity.
Assessing the causal association of pregnancy complications with diabetes and cardiovascular disease
Authors: Xie Yuan , Zhang Jie , Ni Shuang , Li Ji 
Published: June 2024

BackgroundTo the best of our knowledge, numerous observational studies have linked pregnancy complications to increased risks of diabetes and cardiovascular disease (CVD), causal evidence remains lacking. Our aim was to estimate the association of adverse pregnancy outcomes with diabetes and cardiovascular diseases.MethodsA two-sample Mendelian randomization (MR) analysis was employed, which is not subject to potential reverse causality. Data for pregnancy complications were obtained from the FinnGen consortium. For primary analysis, outcome data on diabetes, related traits, stroke, and coronary heart disease (CHD) were extracted from the GWAS Catalog, MAGIC, MEGASTROKE, and CARDIoGRAMplusC4D consortium. The MAGIC and UKB consortium datasets were used for replication and meta-analysis. Causal effects were appraised using inverse variance weighted (IVW), weighted median (WM), and MR-Egger. Sensitivity analyses were implemented with Cochran’s Q test, MR-Egger intercept test, MR-PRESSO, leave-one-out (LOO) analysis and the funnel plot.ResultsGenetically predicted gestational diabetes mellitus (GDM) was causally associated with an increased diabetes risk (OR=1.01, 95% CI=1–1.01, P&lt;0.0001), yet correlated with lower 2-hour post-challenge glucose levels (OR=0.89, 95% CI=0.82–0.97, P=0.006). Genetic liability for pregnancy with abortive outcomes indicated decreased fasting insulin levels (OR=0.97, 95% CI=0.95–0.99, P=0.02), but potentially elevated glycated hemoglobin levels (OR=1.02, 95% CI=1.01–1.04, P=0.01). Additionally, hypertensive disorders in pregnancy was tentatively linked to increased risks of stroke (OR=1.11, 95% CI=1.04–1.18, P=0.002) and CHD (OR=1.3, 95% CI=1.2–1.4, P=3.11E-11). Gestational hypertension might have a potential causal association with CHD (OR=1.11, 95% CI=1.01–1.22, P=0.04). No causal associations were observed between preterm birth and diabetes, stroke, or CHD.ConclusionThe findings of this study provide genetic evidence that gestational diabetes, pregnancy with abortive outcomes, and hypertensive disorders in pregnancy may serve as early indicators for metabolic and cardiovascular risks. These insights are pivotal for the development of targeted screening and preventive strategies.
Association between cathepsins and benign prostate diseases: a bidirectional two-sample Mendelian randomization study
Authors: Cao Hongliang , Liu Bin , Gong Kejian , Wu Hao , Wang Yishu , Zhang Haiyang , Shi Chengdong , Wang Pengyu , Du Hao , Zhou Honglan , Wang Song 
Published: June 2024

ObjectivesThe relationship between cathepsins and prostate cancer (PCa) has been reported. However, there is a lack of research on cathepsins and benign prostate diseases (BPDs). This study investigated the potential genetic link between cathepsins and BPDs through the utilization of Mendelian randomization (MR) analysis to determine if a causal relationship exists.MethodsPublicly accessible summary statistics on BPDs were obtained from FinnGen Biobank. The data comprised 149,363 individuals, with 30,066 cases and 119,297 controls for BPH, and 123,057 individuals, with 3,760 cases and 119,297 controls for prostatitis. The IEU OpenGWAS provided the Genome-wide association data on ten cathepsins. To evaluate the causal relationship between BPDs and cathepsins, five distinct MR analyses were employed, with the primary method being the inverse variance weighted (IVW) approach. Additionally, sensitivity analyses were conducted to examine the horizontal pleiotropy and heterogeneity of the findings.ResultsThe examination of IVW MR findings showed that cathepsin O had a beneficial effect on BPH (IVW OR=0.94, 95% CI 0.89–0.98, P=0.0055), while cathepsin X posed a threat to prostatitis (IVW OR=1.08, 95% CI 1.00–1.16, P=0.047). Through reverse MR analysis, it was revealed that prostatitis had an adverse impact on cathepsin V (IVW OR=0.89, 95% CI 0.80–0.99, P=0.035), while no favorable association was observed between BPH and cathepsins. The results obtained from MR-Egger, weighted median, simple mode, and weighted mode methods were consistent with the findings of the IVW approach. Based on sensitivity analyses, heterogeneity, and horizontal pleiotropy are unlikely to distort the results.ConclusionThis study offers the initial evidence of a genetic causal link between cathepsins and BPDs. Our findings revealed that cathepsin O was beneficial in preventing BPH, whereas cathepsin X posed a potential threat to prostatitis. Additionally, prostatitis negatively affected cathepsin V level. These three cathepsins could be targets of diagnosis and treatment for BPDs, which need further research.
Exploring early DNA methylation alterations in type 1 diabetes: implications of glycemic control
Authors: Čugalj Kern Barbara , Kovač Jernej , Šket Robert , Tesovnik Tine , Jenko Bizjan Barbara , Galhardo Julia , Battelino Tadej , Bratina Nataša , Dovč Klemen 
Published: June 2024

BackgroundProlonged hyperglycemia causes diabetes-related micro- and macrovascular complications, which combined represent a significant burden for individuals living with diabetes. The growing scope of evidence indicates that hyperglycemia affects the development of vascular complications through DNA methylation.MethodsA genome-wide differential DNA methylation analysis was performed on pooled peripheral blood DNA samples from individuals with type 1 diabetes (T1D) with direct DNA sequencing. Strict selection criteria were used to ensure two age- and sex-matched groups with no clinical signs of chronic complications according to persistent mean glycated hemoglobin (HbA1c) values over 5 years: HbA1c&lt;7% (N=10) and HbA1c&gt;8% (N=10).ResultsBetween the two groups, 8385 differentially methylated CpG sites, annotated to 1802 genes, were identified. Genes annotated to hypomethylated CpG sites were enriched in 48 signaling pathways. Further analysis of key CpG sites revealed four specific regions, two of which were hypermethylated and two hypomethylated, associated with long non-coding RNA and processed pseudogenes.ConclusionsProlonged hyperglycemia in individuals with T1D, who have no clinical manifestation of diabetes-related complications, is associated with multiple differentially methylated CpG sites in crucial genes and pathways known to be linked to chronic complications in T1D.
Rare exonic CELSR3 variants identified in Bladder Exstrophy Epispadias Complex
Authors: Jelin Angie C. , Sopko Nikolai , Sobreira Nara , Boyadjiev Simeon A. , Wohler Elizabeth , Morrill Christian , Witmer P. Dane , Michaud Jason , Valle David , Gearhart John , Dicarlo Heather 
Published: June 2024

Introduction/backgroundBladder exstrophy epispadias complex (BEEC) is a rare congenital anomaly of unknown etiology, although, genetic and environmental factors have been associated with its development. Variants in several genes expressed in the urogenital pathway have been reported as causative for bladder exstrophy in human and murine models. The expansion of next-generation sequencing and molecular genomics has improved our ability to identify the underlying genetic causes of similarly complex diseases and could thus assist with the investigation of the molecular basis of BEEC.ObjectiveThe objective was to identify the presence of rare heterozygous variants in genes previously implicated in bladder exstrophy and correlate them with the presence or absence of bladder regeneration in our study population.Patients and MethodsWe present a case series of 12 patients with BEEC who had bladder biopsies performed by pediatric urology during bladder neck reconstruction or bladder augmentation. Cases were classified as “sufficient” or “insufficient” (n = 5 and 7, respectively) based on a bladder volume of greater than or less than 40% of expected bladder size. Control bladder tissue specimens were obtained from patients (n = 6) undergoing biopsies for conditions other than bladder exstrophy. Whole exome sequencing was performed on DNA isolated from the bladder specimens. Based on the hypothesis of de novo mutations, as well as the potential implications of autosomal dominant conditions with incomplete penetrance, each case was evaluated for autosomal dominant variants in a set of genes previously implicated in BEEC.ResultsOur review of the literature identified 44 genes that have been implicated in human models of bladder exstrophy. Our whole exome sequencing data analysis identified rare variants in two of these genes among the cases classified as sufficient, and seven variants in five of these genes among the cases classified as insufficient.ConclusionWe identified rare variants in seven previously implicated genes in our BEEC specimens. Additional research is needed to further understand the cellular signaling underlying this potentially genetically heterogeneous embryological condition.
Two homozygous adjacent novel missense mutations in DYSF gene caused dysferlinopathy due to splicing abnormalities
Authors: Wang Lun , Zhou Yan , Wei Tiantian , Huang Hongyao 
Published: June 2024

Background: Dysferlinopathy is an autosomal recessive disorder caused by mutations in the DYSF gene. This study reported two homozygous adjacent missense mutations in the DYSF gene, presenting clinically with bilateral lower limb weakness and calf swelling. Two homozygous adjacent missense mutations in the DYSF gene may be associated with the development of dysferlinopathy, but the exact mechanism needs further investigation.Methods: A retrospective analysis of clinical data from a dysferlinopathy-affected family was conducted. Peripheral blood samples were collected from members of this family for whole-exome sequencing (WES) and copy number variation analysis. Sanger sequencing was employed to confirm potential pathogenic variants. The Human Splicing Finder, SpliceAI, and varSEAK database were used to predict the effect of mutations on splicing function. The pathogenic mechanism of aberrant splicing in dysferlinopathy due to two homozygous adjacent missense mutations in the DYSF gene was determined by an in vivo splicing assay and an in vitro minigene assay.Results: The proband was a 42-year-old woman who presented with weakness of the lower limbs for 2 years and edema of the lower leg. Two homozygous DYSF variants, c.5628C&gt;A p. D1876E and c.5633A&gt;T p. Y1878F, were identified in the proband. Bioinformatics databases suggested that the mutation c.5628C&gt;A of DYSF had no significant impact on splicing signals. Human Splicing Finder Version 2.4.1 suggested that the c.5633A&gt;T of DYSF mutation caused alteration of auxiliary sequences and significant alteration of the ESE/ESS motif ratio. VarSEAK and SpliceAI suggested that the c.5633A&gt;T of DYSF mutation had no splicing effect. Both an in vivo splicing assay and an in vitro minigene assay showed two adjacent mutations: c.5628C&gt;A p. D1876E and c.5633A&gt;T p. Y1878F in the DYSF gene leading to an Exon50 jump that resulted in a 32-aa amino acid deletion within the protein. Point mutation c.5628C&gt;A p. D1876E in the DYSF gene affected splicing in vitro, while point mutation c.5633A&gt;T p. Y1878F in the DYSF gene did not affect splicing function.Conclusion: This study confirmed for the first time that two homozygous mutations of DYSF were associated with the occurrence of dysferlinopathy. The c.5628C&gt;A p. D1876E mutation in DYSF affected the splicing function and may be one of the contributing factors to the pathogenicity.