bluuebunny/crossref_metadata_2025_split huggingface dataset:
R-codes for Calculating Fluctuation Assay Results and 95% Confidence Intervals Based on Ma-Sandri-Sarkar Maximum Likelihood
Authors: Abdalla Ola , Walker Cameron 
Published: November 2023

Abstract

The Luria-Delbrück fluctuation assay is an essential experiment in calculating mutation rates, especially in genetic and mutation research. Its reliability and accuracy have made it the go-to method for numerous researchers. In this article, we provide R-codes that statistically analyze the assay results more easily and offer the most challenging codes for calculating 95% confidence intervals based on the gold standard method “Ma-Sandri-Sarkar Maximum Likelihood.” Recently, the maximization of the likelihood function through optimization functions in R can be a challenging task. The recursive format of the likelihood function is known to cause memory stack issues. Our findings indicate that utilizing a non-recursive version of the function can increase the tractability of the maximization process. With these codes, future scientists can unlock valuable statistical insights related to the biological mechanisms that drive genetic variation and can, therefore, contribute to developing novel therapeutic interventions and innovative solutions to various biological and medical challenges.
Identification of Plausible Candidates in Prostate Cancer Using Integrated
Machine Learning Approaches
Authors: Kour Bhumandeep , Shukla Nidhi , Bhargava Harshita , Sharma Devendra , Sharma Amita , Singh Anjuvan , Valadi Jayaraman , Sadasukhi Trilok Chand , Vuree Sugunakar , Suravajhala Prashanth 
Published: November 2023

Background:
Currently, prostate-specific antigen (PSA) is commonly used as a prostate
cancer (PCa) biomarker. PSA is linked to some factors that frequently lead to erroneous positive results
or even needless biopsies of elderly people.

Objectives:
In this pilot study, we undermined the potential genes and mutations from several databases
and checked whether or not any putative prognostic biomarkers are central to the annotation. The aim of
the study was to develop a risk prediction model that could help in clinical decision-making.

Methods:
An extensive literature review was conducted, and clinical parameters for related comorbidities,
such as diabetes, obesity, as well as PCa, were collected. Such parameters were chosen with the understanding
that variations in their threshold values could hasten the complicated process of carcinogenesis,
more particularly PCa. The gathered data was converted to semi-binary data (-1, -0.5, 0, 0.5, and 1),
on which machine learning (ML) methods were applied. First, we cross-checked various publicly available
datasets, some published RNA-seq datasets, and our whole-exome sequencing data to find common
role players in PCa, diabetes, and obesity. To narrow down their common interacting partners, interactome
networks were analysed using GeneMANIA and visualised using Cytoscape, and later cBioportal
was used (to compare expression level based on Z scored values) wherein various types of mutation w.r.t
their expression and mRNA expression (RNA seq FPKM) plots are available. The GEPIA 2 tool was
used to compare the expression of resulting similarities between the normal tissue and TCGA databases
of PCa. Later, top-ranking genes were chosen to demonstrate striking clustering coefficients using the Cytoscape-
cytoHubba module, and GEPIA 2 was applied again to ascertain survival plots.

Results:
Comparing various publicly available datasets, it was found that BLM is a frequent player
in all three diseases, whereas comparing publicly available datasets, GWAS datasets, and published
sequencing findings, SPFTPC and PPIMB were found to be the most common. With the assistance
of GeneMANIA, TMPO and FOXP1 were found as common interacting partners, and they were also
seen participating with BLM.

Conclusion:
A probabilistic machine learning model was achieved to identify key candidates between
diabetes, obesity, and PCa. This, we believe, would herald precision scale modeling for easy
prognosis.
ZIP14 Affects the Proliferation, Apoptosis, and Migration of Cervical
Cancer Cells by Regulating the P38 MAPK Pathway
Authors: Jiang Lixia , Xie Ting , Xia Yu , Li Feng , Zhong Tianyu , Lai Mi 
Published: November 2023

Background:
Cervical cancer (CC) remains a major public health concern and is a leading cause of female mortality worldwide. Understanding the molecular basis of its pathogenesis is
essential for the development of novel therapeutic strategies. In this study, we aimed to dissect the
role of a specific molecule, ZIP14, in the initiation and progression of CC.

Methods:
We used Gene Expression Omnibus for target gene identification, while KEGG was
used to delineate CC-related pathways. Proliferation, migration, and apoptosis levels in CC cells
were assessed using CCK8, Transwell, and flow cytometry, respectively. The effect of the target
genes on the in vivo tumorigenesis of CC cells was evaluated using the subcutaneous tumorigenesis
assay.

Results:
ZIP14 (SLC39A14) was found to be underexpressed in CC samples. Our KEGG pathway
analysis revealed the potential involvement of the P38 mitogen-activated protein kinase (MAPK)
pathway in CC pathogenesis. Overexpression of ZIP14 in HeLa and Caski cells increased p38
phosphorylation, inhibited cell growth and migration, and enhanced apoptosis. Conversely, ZIP14
knockdown produced the opposite effects. Importantly, the bioeffects induced by ZIP14 overexpression
could be counteracted by the p38 MAPK pathway inhibitor SB203580. In vivo experiments
further confirmed the influence of ZIP14 on CC cell migration

Conclusion:
Our study is the first to elucidate the pivotal role of ZIP14 in the pathogenesis of CC,
revealing its inhibitory effects through the activation of the p38 MAPK signaling pathway. The
discovery not only provides a deeper understanding of CC's molecular underpinnings, but also
highlights ZIP14 as a promising therapeutic target. As ZIP14 holds significant potential for therapeutic
interventions, our findings lay a robust foundation for further studies and pave the way for
the exploration of novel treatment modalities for cervical cancer.
Transdermal Therapeutic Systems for the Treatment of Alzheimer's
Disease: A Patent Review
Authors: Basso Letícia , Fagundes Silvia Cristina , Staudt Tatiana , da Rosa Karini , Langaro Elizane , Omidian Hamid , Bertol Charise Dallazem 
Published: November 2023

Background:
Two classes of medications are used to treat Alzheimer's disease (AD);
donepezil, galantamine, and rivastigmine are acetylcholinesterase inhibitors, and memantine is a
non-competitive antagonist of the N-methyl-D-aspartate receptor. Although these are typically taken
orally, there are transdermal therapeutic systems (TTSs) commercially available for rivastigmine
and donepezil. The transdermal route has been preferable for guardians/caregivers due to ease of
use, reduced side effects, and improved adherence to therapy.

Objective:
The study aimed to obtain
knowledge of the properties of these drugs and to search for patents relating to the TTS for AD using
the Espacenet platform.

Methods:
The search terms were "rivastigmine AND transdermal AND skin delivery AND Alzheimer’s",
changing the drugs "memantine", "donepezil", and "galantamine", between January 2015
and January 2022. Title and abstract were used to choose patents.

Results:
TTSs present some limit factors in terms of absorption due to skin physiology and the size
of the molecules with established limits of percutaneous penetration (molecular mass of 500 g/mol
and log P of 5). We found 1, 4, 4, and 2 patents for galantamine, rivastigmine, donepezil, and memantine,
respectively. Galantamine TTS seems to be more challenging due to the molecular mass of
287.35 g/mol and logP of 1.8. The permeator of absorption is necessary. Memantine, rivastigmine,
and donepezil present logP of 3.28, 2.3, and 4.27 and molecular weights of 179.30, 250.34, and
415.96 g/mol, respectively.

Conclusion:
TTSs are primarily effective for delivering small molecules. The use of absorption enhancers
and irritation mitigators can be necessary to enhance the performance. The development of
these technologies is essential for the convenience of patients and caregivers.
“Lugar de Indígena é Onde Ela Quiser!”
Authors: Molina Karina , Costa Ribeiro Paula Regina 
Published: November 2023

Este artigo tem por objetivo problematizar a presença das mulheres indígenas em uma universidade federal do sul do Brasil. Por meio de uma investigação narrativa, entendida como o estudo da experiência, entrevistamos[1] cinco acadêmicas indígenas de diferentes cursos da IFES. Propomos uma discussão acerca do papel que a educação superior tem desempenhado, enquanto aliada na luta pela visibilidade das mulheres indígenas, sujeitas marginalizadas da aldeia à academia. Para além da possibilidade de igualdade de oportunidades, as ações afirmativas resultam na qualificação universitária não apenas para a causa indígena, mas também para o retorno às aldeias. Ao mesmo tempo, estar na universidade implica às acadêmicas indígenas resistirem não apenas a sua realidade nas comunidades, mas na universidade também.

[1] As entrevistas começaram após aprovação do projeto pelo Comitê de Ética em Pesquisa da Universidade e pela Comissão Nacional de Ética em Pesquisa, por meio do parecer nº 4.274.905, Certificado de Apresentação de Apreciação Ética (CAAE) 34247320.6.0000.5324.
Extracting Clinical Information From Japanese Radiology Reports Using a 2-Stage Deep Learning Approach: Algorithm Development and Validation
Authors: Sugimoto Kento , Wada Shoya , Konishi Shozo , Okada Katsuki , Manabe Shirou , Matsumura Yasushi , Takeda Toshihiro 
Published: November 2023

AbstractBackgroundRadiology reports are usually written in a free-text format, which makes it challenging to reuse the reports.ObjectiveFor secondary use, we developed a 2-stage deep learning system for extracting clinical information and converting it into a structured format.MethodsOur system mainly consists of 2 deep learning modules: entity extraction and relation extraction. For each module, state-of-the-art deep learning models were applied. We trained and evaluated the models using 1040 in-house Japanese computed tomography (CT) reports annotated by medical experts. We also evaluated the performance of the entire pipeline of our system. In addition, the ratio of annotated entities in the reports was measured to validate the coverage of the clinical information with our information model.ResultsThe microaveragedF1-scores of our best-performing model for entity extraction and relation extraction were 96.1% and 97.4%, respectively. The microaveragedF1-score of the 2-stage system, which is a measure of the performance of the entire pipeline of our system, was 91.9%. Our system showed encouraging results for the conversion of free-text radiology reports into a structured format. The coverage of clinical information in the reports was 96.2% (6595/6853).ConclusionsOur 2-stage deep system can extract clinical information from chest and abdomen CT reports accurately and comprehensively.
La nouvelle sociologie de l’enfance et les droits des enfants
Authors: Thibault Jacqueline 
Published: November 2023

This article focuses on childhood and more specifically on children's rights, from the perspective of the new sociology of childhood. Although children's rights advocates and proponents of the new sociology of childhood both aspire to a better understanding of childhood while striving to improve the lives of children, collaborative work between the two disciplines is rare (Freeman, 1998). I will therefore attempt to answer the following question: how are children's rights addressed in the new sociology of childhood and what are its implications for research, policies, and practices in social work?
Keywords: child, children's rights, new sociology of childhood, social work, best interests of the child, participation
PEMANFAATAN TANAMAN PENINGKAT DAYA TAHAN TUBUH PADA MASYARAKAT DI PROVINSI KALIMANTAN BARAT SELAMA PANDEMI COVID-19
Authors: Awaliyah Nurdianti , Qurbaniah Mahwar 
Published: November 2023

Selama pandemi Covid-19, masyarakat disarankan untuk mengkonsumsi makanan dan minuman yang dapat menjaga ataupun meningkatkan daya tahan tubuh. Di Indonesia, banyak terdapat tanaman obat keluarga (TOGA) yang dapat menjaga atau meningkatkan daya tahan tubuh. Tujuan penelitian ini adalah untuk mengetahui tanaman obat apa saja yang dimanfaatkan oleh masyarakat di Provinsi Kalimantan Barat untuk meningkatkan daya tahan tubuh selama pandemi Covid-19. Metode penelitian dilakukan dengan metode survei dengan 60 responden yang diambil dengan teknik simple random sampling. Instrumen penelitian yang dibutuhkan adalah angket dan literatur-literatur lainnya yang mendukung. Dari hasil kajian literasi sebelumnya ada sekitar 19 tanaman obat yang dapat menjaga ataupun meningkatkan daya tahan tubuh yang kemudian disurvei kepada responden. Hasil penelitian menunjukkan tanaman untuk menjaga daya tahan tubuh yang dimanfaatkan oleh masyarakat Provinsi Kalimantan Barat dengan rincian jahe 100 %, jahe merah 72 %, temu lawak 77 %, temu manga 40 %, kunyit 98 %, kencur 91 %, lengkuas 91%, cengkeh 75 %, jintan hitam 54 %, bawang putih 95 %, cabe merah 80 %, pegagan 56 %, meniran 23 %, sambiloto 28 %, kelor 54 %, mengkudu 72 %, kantong semar 23 %, kelapa 100 % dan jambu biji 100%
Analisis Kandungan Karbon di Taman Kehati PT Chandra Asri Cilegon
Authors: Marianingsih Pipit , Mahrawi Mahrawi , Purnama Dania , Oktaviani Hesti , Amelia Reza , Eliyana Siti , Karahayon Yoseph Sugiharto , Febrio Eren Putra 
Published: November 2023

CO2 emissions continue to increase every year. The increase in CO2 emissions in Indonesia is caused by an increase in greenhouse gases and the production of CO2 emissions is inseparable from human activities. One of the efforts to reduce CO2 emissions can be done through the Biodiversity Park (Kehati) development program. This study aims to determine the estimation of biomass, carbon stocks and carbon dioxide absorption in PT Chandra Asri's biodiversity park as one of the efforts to reduce carbon emissions. The method used in collecting data on biomass is a non-destructive sampling method using allometric equation analysis to extrapolate biomass. The results showed that the total estimated biomass of all standing categories was 2745 tons/ha, the total carbon stock was 1290.15 tons/ha and the total CO2 absorption was 4734.85 tons/ha. This shows that the carbon stock in Taman Kehati PT. Chandra Asri Cilegon is in the high category because it spans more than 100 tonnes/ha so that PT. Chandra Asri Cilegon can maximize its function as a carbon absorption and storage area to reduce CO2 emissions.
Keywords: Allometric equations, biodiversity park, biomassa, carbon dioxide absorption, carbon

Abstrak
Emisi CO2 terus mengalami peningkatan di tiap tahunnya. Meningkatnya emisi CO2 di Indonesia diakibatkan oleh meningkatnya gas rumah kaca (GRK) dan produksi emisi CO2 ini tidak terlepas dari aktivitas yang dilakukan oleh manusia. Salah satu upaya penurunan emisi CO2 dapat dilakukan melalui program pembangunan Taman Keanekaragaman Hayati (Kehati). Penelitian ini bertujuan untuk mengetahui perkiraan estimasi biomassa, cadangan karbon dan serapan karbon dioksida di taman kehati PT Chandra Asri sebagai salah satu upaya dalam penanganan untuk mengurangi emisi karbon. Metode yang dipakai dalam pengambilan data biomassa yaitu metode nondestructive sampling menggunakan analisis persamaan allometrik untuk mengekstrapolasi biomassa. Hasil penelitian menunjukan jumlah estimasi biomassa semua kategori tegakan sebesar 2745 ton/ha, jumlah cadangan karbon sebesar 1290,15 ton/ha dan jumlah serapan CO2 sebesar 4734,85 ton/ha. Hal ini menunjukkan bahwa cadangan karbon pada Taman Kehati PT. Chandra Asri Cilegon berada dalam kategori tinggi karena berada direntang lebih dari 100 ton/ha sehingga Taman Kehati PT. Chandra Asri Cilegon dapat memaksimalkan fungsinya sebagai salah satu kawasan penyerapan dan penyimpanan karbon untuk untuk mengurangi emisi CO2.
Kata kunci: Biomassa, cadangan karbon, persamaan allometrik, serapan karbondikosida, taman kehati
Karakter Morfologi Bunga Dan Buah Putat (Barringtonia acutangula (L.) Gaertn.)
Authors: Dewi Syntiya , Hariyadi Bambang , Ihsan Mahya 
Published: November 2023

This research delves into the morphological characteristics of Putat (Barringtonia acutangula (L.) Gaertn.) in its natural habitat at Tangkas Lake, Muaro Jambi Regency, Jambi Province. In a landscape where water levels ebb and flow, Putat predominantly swathes the lake, enriching its visual allure and nurturing the area's development into a tourist attraction. The captivating aesthetics of Putat, marked by its distinct and briefly blossoming flowers, enhance the lake's appeal, drawing community interest and tourism. The study is meticulous, utilizing purposive sampling at two strategic locations and employing descriptive analysis supported by visual representations and tables. The findings unveil detailed insights into the plant’s flowers, fruits, and seeds. Putat’s flowers are found to be vibrant, unlimited compound entities, while its fruit evolves from a verdant to a purplish hue upon maturity, encompassing a singular, resilient seed. This in-depth exploration contributes valuable knowledge to the limited existing information, facilitating a deeper understanding of Putat’s unique ecological presence and biodiversity at Tangkas Lake.
Keywords: Barringtonia acutangula, Putat, Danau Tangkas, Flower, Morphological character

Abstrak
Penelitian ini mengkaji Putat (Barringtonia acutangula (L.) Gaertn.) di habotat alaminya di Danau Tangkas, Kabupaten Muaro Jambi, Provinsi Jambi. Putat yang tumbuh alami di danau memperkaya ekosistem lokal dengan keindahan flora uniknya, dan meningkatkan potensi danau sebagai destinasi wisata. Kajian ini berfokus pada karakterisasi morfologi bunga, buah, dan biji putat, untuk mengisi kekurangan informasi mengenai proses reproduksi tumbuhan ini. Data dikumpulkan menggunakan metode sampling purposif dilanjutkan dengan analisis secara deskriptif. Hasil penelitian menunjukkan bunga putat sebagai bunga majemuk tak terbatas dengan corolla merah yang menarik, dan struktur yang kompleks. Buah putat, berbentuk lonjong dan berkembang dari hijau menjadi hijau keunguan saat matang, serta mengandung biji tunggal yang kokoh. Temuan ini memberikan kontribusi penting dalam pemahaman lebih lanjut mengenai biodiversitas dan adaptasi ekologi Putat di habitatnya.
Kata kunci: Barringtonia acutangula, Putat, Danau Tangkas, Bunga, Morfologi
ANALISIS KEPUASAN PETANI PADI SAWAH TERHADAP KINERJA PPL DI KECAMATAN SEKERNAN KABUPATEN MUARO JAMBI
Authors: Muchlis Fuad , Nadyah Nadyah , Lubis Arsyad 
Published: November 2023

Penyuluh dituntut memiliki pengetahuan dan kecakapan yang cukup didalam berkomunikasi dengan petani untuk memberikan penjelasan yang dapat menghilangkan kebimbangan petani dalam penerapan informasi teknologi baru yang disampaikan berkaitan dengan usahataninya.Penelitian ini bertujuan untuk 1) mengetahui tingkat kepentingan terhadap kinerja PPL dan 2) untuk melihat tingkat kepuasan petani padi sawah terhadap atribut-atribut kinerja yang telah dilaksanakan oleh PPL di Kecamatan Sekernan Kabupaten Muaro Jambi. Penelitian ini dilakukan menggunakan metode kuantitatif dengan mengunakan alat analisis Importance Performance Analysis (IPA). Hasil penelitian menunjukkan bahwa 1) tingkat kepentingan petani terhadap kinerja PPL dikategorikan tinggi. 2) Tingkat kepuasan petani terhadap atribut-atribut kinerja PPL dikategorikan mendekati puas
The Apollo 17 Regolith: Induced Thermoluminescence Evidence for Formation by a Single Event ~100 Million Years Ago and Possibly the Presence of Tycho Material.
Authors: Sehlke Alexander , Sears Derek 
Published: November 2023

We explored the geological history of the Taurus-Littrow Valley at the
Apollo 17 landing site through the induced thermoluminescence (TL)
properties of regolith samples collected from the foothills of the
Northern and Southern Massifs, near the landing site, and the deep drill
core taken in proximity to the landing site. The samples were recently
made available by NASA through the Apollo Next Generation Sample
Analysis program, in anticipation of the forthcoming Artemis missions.
We found that the two samples from the foothills of the massifs exhibit
induced TL values approximately four times higher than those of the
valley samples. This observation is consistent with their elevated
plagioclase content, indicating their predominantly highland material
composition. Conversely, the valley samples display induced TL values
characteristic of lunar mare material. The samples from the deep drill
core demonstrate uniform induced TL properties, despite originating from
depths of up to 3 meters. Notably, one of the samples from the lower
section of the deep drill core presents anomalous induced TL readings.
This anomaly coincides with elevated levels of low-potassium KREEP,
along with reduced quantities of anorthositic gabbro and orange glass,
and could be due to the traces of phosphate minerals. Alternatively,
this observation raises the possibility that this sample contains Tycho
impact material.
The induced TL data is consistent with the regolith, extending to a
depth of at least 3 meters, having been deposited by a singular event
approximately 100 million years ago. This timing aligns with the
hypothesized formation of the Tycho crater.
The Effect Of Time Fermentation On The Physical Quality Of Cow’s Rumen Content Silage
Authors: Ton Jusril Wina , Wie Lawa Emma Dyelim , Hilakore Maritje Aleonor , Lazarus Edwin J.L 
Published: November 2023

The study aimed to determine the effect of fermentation time on the physical quality of cow’s rumen content silage. The study used an experimental method based on a completely randomized design (CRD) with 4 treatments of incubation time and 4 replications. The composition of the silage ingredients was as follows: cow’s rumen contents 60% + rice bran 35% + palm sugar 5% + local microorganisms 40 ml. Treatment of the fermentation time was P1: four weeks, P2: six weeks, P3: eight weeks, and P4: ten weeks. The variables observed were color, texture, odor, fungus, and cow’s rumen content silage pH. The results of the Kruskall Wallis Test analysis showed that the treatment had a very significant effect (P <0.01) on texture and odor. Still, they had no significant effect (P>0.05) on color and fungus. The results of ANOVA showed that the treatment had a very significant effect (P<0.01) on the pH value. Based on the results it can be concluded that the different fermentation times affected the texture, odor, and pH value, but not affect the color and fungus existence. The best fermentation time for this research is 8 weeks.