Miracle-dz/UniFAR-FTUs huggingface dataset:
A Reconsideration of the Effect of Procyanidin on the Assembly of Collagen Type I

In order to elucidating the exact effect mechanism of polyphenols on the assembly of collagen, the assembled architectures of collagen treated with different amounts of procyanidin (PA) were investigated in details. The assembled morphologies of collagen were greatly influenced by the content of PA according to atomic force microcopy (AFM) images. When the content of PA was more than 20% (w/w), the fibrillar morphologies were substituted by globular aggregates, which were driven by the intense hydrogen bonding action originating from PA. While the formation of the non-fibrous aggregates was due to the coiling and entangling of flexible collagen molecules rather than their gelatinization based on the appearance of typical adsorption peaks at 222nm and 197nm on circular dichroism (CD) spectra. After being crosslinked by glutaraldehyde (GA), not only the diameters but also the lengths of fibrils increased. Unfortunately, the fibrillogenesis was still inhibited when the collagen suffered from 20% PA firstly and then 4% GA. Conversely, the fibrous morphologies of the fibrils stabilized by 4% GA and then underwent 20% PA maintained well, in spite of accompanying with grievous intertwining. This difference was derived from the change of flexibilities of collagen before and after being crosslinked by GA. Additionally, the differential scanning calorimeter (DSC) analysis confirmed the PA had no positive effect on the improvement of thermal stability of hydrous collagen, whereas the denaturation temperature of hydrated collagen stabilized by 4% GA increased from 40 °C to 80 °C.
Population Dynamics Model to Inform Harvest Management of a Small Elk Herd in Central New Mexico

Crop depredation by wildlife is a frequent concern for natural resource managers and mitigation of this issue is often an important task for wildlife agencies. Elk Cervus elaphus and other ungulate species have depredated corn Zea mays at Bosque del Apache National Wildlife Refuge, New Mexico, USA, interfering with the ability of the Refuge to provide sufficient supplemental nutrition to overwintering sandhill cranes Antigone canadensis and geese (Anatidae). We estimated annual adult survival and calf recruitment rates of elk from 2011 to 2013 at Bosque del Apache National Wildlife Refuge. Natural adult survival (excludes human-related mortalities) was high (mean = 98.3%; 95% CI = 95.0–100.0%). Calf recruitment was lower than in some populations, and ranged from 13.0 to 36.7 calves : 100 cows at time of recruitment (March and April) with a mean of 21.9 (SD =12.9). Using this information, we constructed a harvest management model to determine annual harvest quotas required to stabilize the growth of the elk herd on the Refuge. The female segment of the herd is growing at an annual rate of 9.0% (95% CI = −1.1–24.1%). To stabilize the growth rate of the female elk population, 8.0% (95% CI = −1.1–19.4%) of the cows would need to be harvested annually. We estimated an adult elk abundance of 40.0 (SE = 4.57; 95% CI = 33.8–52.6) in 2012 and 61.1 (SE = 7.21; 95% CI = 49.9–78.8) in 2013. Our harvest management model provides Refuge staff, who ultimately intend to improve corn yield, with valuable information needed to stabilize the elk herd. Further, our approach outlines a simple, easily implemented modeling technique that can be used for the management of other ungulate herds.
Longitudinally Dependent Low‐Latitude Ionospheric Disturbances Linked to the Antarctic Sudden Stratospheric Warming of September 2019

The strongest Southern Hemisphere minor sudden stratospheric warming (SSW) in the last 40 years occurred in September 2019 and resulted in unprecedented weakening of the stratospheric polar vortex. Ionospheric total electron content (TEC) observations are used to provide an overview of statistically significant anomalies in the low‐latitude ionosphere during this event. Quasi‐semidiurnal perturbations of TEC are observed in response to the SSW, similar to those seen during Northern Hemisphere SSWs. Analysis indicates the existence of quasi‐periodic oscillations in TEC in the crests of the equatorial ionization anomaly, with strong 5‐ to 6‐day and 2‐ to 3‐day periodicities. Ionospheric anomalies from the combined effects of multiple mechanisms exceed a factor of 2, comparable to the strongest anomalies associated with Northern Hemisphere SSWs. These results also indicate a remarkable longitudinal variation in the character and magnitude of variations that could be related to a modulation of the non‐migrating diurnal tide.
Lipid associated polygenic enrichment in Alzheimer’s disease

Cardiovascular (CV) and lifestyle associated risk factors (RFs) are increasingly recognized as important for Alzheimer’s disease (AD) pathogenesis. Beyond the ∊4 allele of apolipoprotein E (APOE), comparatively little is known about whether CV associated genes also increase risk for AD (genetic pleiotropy). Using large genome-wide association studies (GWASs) (total n > 500,000 cases and controls) and validated tools to quantify genetic pleiotropy, we systematically identified single nucleotide polymorphisms (SNPs) jointly associated with AD and one or more CV RFs, namely body mass index (BMI), type 2 diabetes (T2D), coronary artery disease (CAD), waist hip ratio (WHR), total cholesterol (TC), low-density (LDL) and high-density lipoprotein (HDL). In fold enrichment plots, we observed robust genetic enrichment in AD as a function of plasma lipids (TC, LDL, and HDL); we found minimal AD genetic enrichment conditional on BMI, T2D, CAD, and WHR. Beyond APOE, at conjunction FDR < 0.05 we identified 57 SNPs on 19 different chromosomes that were jointly associated with AD and CV outcomes including APOA4, ABCA1, ABCG5, LIPG, and MTCH2/SPI1. We found that common genetic variants influencing AD are associated with multiple CV RFs, at times with a different directionality of effect. Expression of these AD/CV pleiotropic genes was enriched for lipid metabolism processes, over-represented within astrocytes and vascular structures, highly co-expressed, and differentially altered within AD brains. Beyond APOE, we show that the polygenic component of AD is enriched for lipid associated RFs. Rather than a single causal link between genetic loci, RF and the outcome, we found that common genetic variants influencing AD are associated with multiple CV RFs. Our collective findings suggest that a network of genes involved in lipid biology also influence Alzheimer’s risk.
Decadal‐Scale Recovery of Carbon Stocks After Wildfires Throughout the Boreal Forests

Boreal forests store 30% of the world's terrestrial carbon (C). Consequently, climate change mediated alterations in the boreal forest fire regime can have a significant impact on the global C budget. Here we synthesize the effects of forest fires on the stocks and recovery rates of C in boreal forests using 368 plots from 16 long‐term (≥100 year) fire chronosequences distributed throughout the boreal zone. Forest fires led to a decrease in total C stocks (excluding mineral soil) by an average of 60% (range from <10% to >80%), which was primarily a result of C stock declines in the living trees and soil organic layer. Total C stocks increased with time since fire largely following a sigmoidal shape Gompertz function, with an average asymptote of 8.1 kg C m−2. Total C stocks accumulated at a rate of 2–60 g m−2 yr−1 during the first 100 years. Potential evapotranspiration (PET) was identified as a significant driver of C stocks and their post‐fire recovery, likely because it integrates temperature, radiation, and the length of the growing season. If the fire return interval shortens to ≤100 years in the future, our findings indicate that many boreal forests will be prevented from reaching their full C storage potential. However, our results also suggest that climate warming‐induced increases in PET may speed up the post‐fire recovery of C stocks.
Prior precision modulates the minimisation of prediction error in human auditory cortex

The predictive coding model of perception proposes that successful representation of the perceptual world depends upon cancelling out the discrepancy between prediction and sensory input (i.e., prediction error). Recent studies further suggest a distinction between prediction error associated with non-predicted stimuli of different prior precision (i.e., inverse variance). However, it is not fully understood how prediction error from different precision levels is minimised in the predictive process. The current research used magnetoencephalography (MEG) to examine whether prior precision modulates the cortical dynamics of the making of perceptual inferences. We presented participants with cycles of repeated tone quartets which consisted of three prime tones and one probe tone. Within each cycle, the three prime tones remained identical while the probe tones changed at some random point (e.g., from repetition of 123X to repetition of 123Y). Therefore, the repetition of probe tones can reveal the development of perceptual inferences in low and high precision contexts depending on its position within the cycle. We found that the two conditions resemble each other in terms of N1m modulation (as both were associated with N1m suppression) but differ in terms of N2m modulation. While repeated probe tones in low precision context did not exhibit any modulatory effect, repeated probe tones in high precision context elicited a suppression and rebound of the N2m source power. The differentiation suggested that the minimisation of prediction error in low and high precision contexts likely involves distinct mechanisms.
The Effects of Licorice Root Powder (Glycyrrhriza glabra) on Performance, Serum Parameters, Egg Yolk Cholesterol and Antioxidant Capacity of Laying Japanese Quail

This study was conducted with the objectives to determine the effects of licorice root powder (Glycyrrhriza glabra) on performance, serum parameters, egg yolk cholesterol and antioxidant capacity in laying Japanese quail. Two hundred and forty 10-wk-old Japanese quails were randomly assigned to four dietary groups, each one four times replicated with fifteen quails per dietary groups. Control group fed the basal diet; other groups were fed basal diet supplemented with 0, 0.5, 1.0 and 1.5% licorice root powder. There were no significant differences in terms of final live weight, feed intake, feed conversion ratio, egg weight, serum cholesterol, triglyceride and High-Density Lipoprotein (HDL) concentration between treatment groups. Egg production was higher in control group and 0.5% licorice root powder supplemented groups. 1.0% licorice root powder supplemented group had lower egg production rate. Licorice root powder supplementation decreased Low Density Lipoprotein (LDL) concentration and increased glucose concentration significantly. Licorice root powder supplementation increased total antioxidant status (TAS) and reduced total oxidant status (TOS) and oxidative stress index (OSI). It was concluded from this study that supplementation of licorice root powder at the level of 0.5, 1.0 and 1.5% to the feed of laying quails had no adverse effects on performance. Licorice root powder supplementation can be used to reduce cholesterol level and increase antioxidant status in quails.
Dissecting the functions of atr in replication fork stability

Genome maintenance is required for cellular viability, and failure to preserve genomic integrity is associated with an increased risk of diseases, such as cancer. To ensure genomic stability, cells have checkpoints that control cell cycle progression in the event of DNA damage or incomplete DNA replication. The DNA replication checkpoint is regulated by the ATR-CHK1 pathway that stabilizes stalled replication forks and prevents their collapse into DNA double-strand breaks (DSBs). Two distinct models have been proposed to explain how ATR stabilizes stalled forks: 1) through local modulation of fork remodelers, such as SMARCAL1 inhibition, and 2) through inhibition of CDK-dependent pathways, such as inhibition of the AURKA-PLK1 pathway, which prevent cell cycle progression. However, it remains unclear which stabilization function is essential for fork stability and whether specific sites in the genome depend on one function over the other. In an effort to test if an essential part of fork stabilization is mediated through inhibiting CDK-dependent pathways, such as inhibiting premature activation of the AURKA-PLK1 pathway, we established a system to hyper-activate the AURKA-PLK1 pathway to determine if it is sufficient to cause fork collapse. We found that fork collapse was not achievable solely through Aurora A overexpression nor with overexpression of its coactivators, TPX2 and BORA, but rather that CDK1 activation was also required. To test if CDK1-activation is sufficient to promote fork collapse, we inhibited WEE1, which short-circuits the cell cycle checkpoint function of ATR without inhibiting its fork-proximal activity. Using flow cytometry based fork collapse assays and genome-wide detection of RPA accumulation using RPA ChIP-Seq, we show that WEE1 and ATR inhibition cause similar levels of fork collapse at overlapping genomic locations in a CDK1-depdendent manner under conditions of partial replication inhibition (low dose aphidicolin). Notably, treatment with WEE1 inhibitor (WEE1i) alone was also sufficient to cause replication fork collapse, and did so more rapidly and to a higher degree than treatment with ATR inhibitor (ATRi) alone. Interestingly, clear differences in site specificity were observed when WEE1i was combined with ATRi, suggesting that particular sites in the genome may be slightly more dependent on the local functions of ATR than others. Thus, cell cycle checkpoint abrogation by WEE1i is sufficient to cause replication fork collapse in a manner similar to ATRi; however, site-specific roles for ATR remain. Together our findings indicate that the cell cycle checkpoint of ATR is key in stabilizing replication forks at a majority of sites in the genome. These findings could be leveraged to develop cancer treatments that exploit combinations of oncogenic genomic breakage signatures with that of WEE1 or ATR inhibitors. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology This dissertation is available at ScholarlyCommons: https://repository.upenn. edu/edissertations/3070 First Advisor Eric J. Brown
A rare case of primary extrauterine endometrial stromal sarcoma involving the sigmoid colon

Endometrial stromal sarcoma (ESS) is a rare type of endometrial mesenchymal neoplasm that commonly affects the uterus. The authors report an unusual case of sigmoid colonic ESS. A 46-year-old woman, complaining hematochezia and chronic abdominal pain, was diagnosed with ESS in the sigmoid colon. The patient underwent laparoscopic sigmoid colon resection and had no adjuvant therapy postoperatively. Two years later, the patient developed a new symptom of irregular vaginal bleeding with cervical myoma measuring about 9.0 cm, then a laparoscopic hysterectomy with a bilateral salpingo-oophorectomy was performed. Microscopically, the mass was diagnosed as adenomyosis and low-grade ESS. This case highlights the rarity of extrauterine ESS in the sigmoid colon, especially in the absence of a known history of primary uterine ESS. If the patient underwent prophylactic hysterectomy and adnexectomy after sigmoid colon resection, the recurrence would have been probably delayed.
Description of the postmarsupial manca stages of Armadillidium granulatum (Crustacea, Isopoda, Oniscidea)

ABSTRACT The development of the postmarsupial manca stages of Armadillidium granulatum Brandt, 1833 was studied in detail by morphological analysis. Ovigerous females were reared separately under controlled conditions, allowing us to follow the stages of development from release from the marsupium until the appearance of the first juvenile stage, identified by the full development of the seventh pair of pereopods. Each newborn was followed to record the subsequent moults that identify the three postmarsupial manca stages. Manca stage M I had a mean duration of 6 h, manca stage M II 15 days, and manca stage M III 32 days. The cephalothorax width was measured to provide a growth measure for each stage. The mean values of the cephalothorax width were: 0.512 mm (± 0.083 SD) for M I, 0.677 mm (± 0.058 SD) for M II and 1.194 mm (± 0.079 SD) for M III. The morphological modifications in the three postmarsupial manca stages were described, the body parts illustrated, and SEM images taken. The distinguishing characteristics among mancas were discussed, and comparisons made with manca stages of other terrestrial isopod species.
Systematic extraction and characterization of β-glucan from the industrial brewing yeast (Saccharomyces cerevisiae) waste material and the immunomodulatory studies on TNF-α and IL-6 cytokine balance of the mouse macrophage cell lines

Objectives: The aim of this investigation was to create value to the industrial waste production by systematic extraction and purification of β-glucan from the industrial brewing yeast ( Saccharomyces cerevisiae ) waste material. In addition, the immunological activity of the obtained β-glucan was also evaluated. Methods: The β-glucan from the yeast waste material of the brewing production was isolated by cell autolysis fractioning, solvent extraction and drying. The obtained β-glucan was characterized by HPLC, NMR and comparison with information in the literature. The characterized β-glucan was then examined for its immunomodulatory activity on RAW 264.7 cell. Results: The optimal extraction method of β-glucan from the brewing waste material showed high extraction yield (13.14% w/w). In addition, the immunomodulatory study on RAW 264.7 cell lines showed that the isolated β-glucan could suppress the TNF-α and IL-6 production in the cell lines at 6 h and 24 h, compared to the LPS control.
Developing pre-service O&M specialists’ reflective practices to improve problem-solving opportunities during instruction

The ability of instructors to promote problem-solving abilities is an important pedagogical skill. Providing well-planned problem-solving opportunities is especially vital in orientation and mobility (O&M) lessons. During personnel preparation programs, pre-service O&M specialists would benefit from developing a keen awareness of how well they encourage problem-solving in their instruction. This mixed-methods study reports on a process in which nine pre-service O&M specialists engaged during their blindfold techniques course. Each participant taught two lessons to a peer in their course, engaging in a retroactive think-aloud after each lesson. The process focused participants on the types of questions they asked to promote thinking and engaged them in reflection on how well the lesson met their intended objectives. Results indicated qualitative benefits noted by the participants of engaging in the process and also highlighted a need for further work with pre-service O&M specialists on question asking and allowing problem-solving and thinking opportunities during basic lessons.
A comparison of male and female headed house holding of orphans and vulnerable children in Nigeria

Literature revealed the prognosis of vulnerability of households headed by females in general is poor. One can imagine the situation in households occupied by orphans and vulnerable children (OVC). Orphan-hood may arise from the death of one or both parents. This study compared the situation in male and female headed households among OVC households in three selected communities in Nigeria. The survey was carried out between May and July 2016, by the Association of Reproductive and Family Health (ARFH), the implementer of Local partners for OVC in Nigeria (LOPIN) Region 1 project. A cross-sectional study of 3,706 OVC households was undertaken prior implementation of ARFH)-LOPIN 1} project in Lagos-1,299 households, Rivers-912 and Akwa-Ibom-1,495 households. The National Vulnerable Assessment Questionnaire developed by Bamgboye et al. was used to identify the vulnerable households. The analysis of data collected showed that the proportion of females heading households was 56%. Also, the females heading households were younger, poorer and their OVC less likely to access health educational services as well as less food secured. The high poverty level in Nigeria demands special attention to the health, education, nutrition and socio-economic needs of OVC (particularly those headed by females), for them to have a meaningful life. Key words: Nigeria, orphans and vulnerable children, household, female headship.
Scaling up Deliberation: Testing the Potential of Mini‐Publics to Enhance the Deliberative Capacity of Citizens

: This paper tests the possibility of embedding the beneﬁts of minipublic deliberation within a wider voting public. We test whether a statement such as those derived from a Citizens’ Initiative Review (CIR) can inﬂuence voters who did not participate in the pre-referendum minipublic deliberation. This experiment was implemented in advance of the 2018 Irish referendum on blasphemy, one of a series of social-moral referendums following the recommendations of a deliberative assembly. This is the ﬁrst application of a CIR-style voting aid in a real world minipublic and referendum outside of the US and also the ﬁrst application to what is principally a moral question. We found that survey respondents exposed to information about the minipublic and its ﬁndings signiﬁcantly increased their policy knowledge. Further, exposing respondents to minipublic statements in favour and against the policy measure increased their empathy for the other side of the policy debate.
The Analysis of Online Brand Community, Online Perceived Brand Reputation, Brand Trust, Brand Loyalty at Cafe Businesses Based in Surabaya

The internet has become a human lifestyle. Many business people took advantage of this opportunity to market their business by using social media marketing strategy on Facebook or Instagram. Activities in the online brand community on social media platforms could build consumer perceptions of a brand inside the online world and would form a belief in the brand that ultimate to loyalty. Therefore, social media marketing must be known for its effectiveness. This study aims to determine the influence of the online brand community on online perceived brand reputation, brand trust, and brand loyalty at cafes in Surabaya. The method used in this study is quantitative by spreading the questionnaires to 240 respondents of college students both online and offline. The research using purposive sampling technique and the sample used in this research is the consumers of De Mandailing Cafe & Eatery, Panties Pizza, and Warunk Upnormal in Surabaya where the three cafes are considered to represent the whole cafes with the same quality, consumers, service system, and price range. From the results of this study, it can be concluded that online brand community has a significant impact on brand loyalty through online process perceived brand reputation and brand trust.