Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulating the Large-Scale Erosion of Genomic Privacy Over Time

The dramatically decreasing costs of DNA sequencing have triggered more than a million humans to have their genotypes sequenced. Moreover, these individuals increasingly make their genomic data publicly available, thereby creating privacy threats for themselves and their relatives because of their DNA similarities. More generally, an entity that gains access to a significant fraction of sequenced genotypes might be able to infer even the genomes of unsequenced individuals. In this paper, we propose a simulation-based model for quantifying the impact of continuously sequencing and publicizing personal genomic data on a population's genomic privacy. Our simulation probabilistically models data sharing and takes into account events such as migration and interracial mating. We exemplarily instantiate our simulation with a sample population of 1,000 individuals and evaluate the privacy under multiple settings over 6,000 genomic variants and a subset of phenotype-related variants. Our findings demonstrate that an increasing sharing rate in the future entails a substantial negative effect on the privacy of all older generations. Moreover, we find that mixed populations face a less severe erosion of privacy over time than more homogeneous populations. Finally, we demonstrate that genomic-data sharing can be much more detrimental for the privacy of the phenotype-related variants.
A dual-band and dual-polarization antenna with two nested triangular rings

In this letter, a low-profile dual-band dual-polarization antenna is proposed. The antenna consists of two nested triangular rings. By simultaneously excited by a rectangular strip, two orthogonal modes of the triangular rings are excited at two frequencies to realize dual polarization characteristics. By varying the vertex angle of the triangular rings, the frequency ratio of the two modes could be adjustable. The simulated −10 dB reflection coefficient bandwidth of the two modes are 130 MHz in lower frequency band and 170 MHz in upper frequency band for vertical and horizontal polarization, respectively. The proposed antenna has advantages of simple structure, low cross polarization and low cost.
The Effects of Comprehension-Test Expectancies on Metacomprehension Accuracy

A set of four experiments assessed the effects of establishing a comprehension-test expectancy (in contrast to a memory-test expectancy) on relative metacomprehension accuracy. Typically readers show poor relative metacomprehension accuracy while learning from text (i.e., they are unable to discriminate topics they have understood well from topics they have understood poorly). In the first experiment, both readers who were given no test expectancy and those who were given a memory-test expectancy made judgments that were more predictive of performance on memory tests than inference tests. However, readers who were given a comprehension-test expectancy made judgments that were more predictive of inference-test performance. This effect was replicated and extended in two additional experiments that showed an effect of comprehension-test expectancy even when no example test items were provided, and when the expectancy was established only after reading. A fourth experiment showed that establishing a comprehension-test expectancy still had an effect on accuracy even when metacomprehension accuracy was already being improved via a self-explanation activity. The results show robust and reliable benefits to metacomprehension accuracy from a comprehension-test expectancy that serves as portable knowledge that learners can apply to monitoring future learning from text.
In vitro culture of murine megakaryocytes from fetal liver-derived hematopoietic stem cells

Abstract Megakaryocytes (MKs) are specialized precursor cells committed to producing and proliferating platelets. In a cytoskeletal-driven process, mature MKs generate platelets by releasing thin cytoplasmic extensions, named proplatelets, into the sinusoids. Due to knowledge gaps in this process and mounting clinical demand for non-donor-based platelet sources, investigators are successfully developing artificial culture systems to recreate the environment of platelet biogenesis. Nevertheless, drawbacks in current methods entail elaborate procedures for stem cell enrichment, extensive growth periods, low MK yield, and poor proplatelet production. We propose a simple, robust method of primary MK culture that utilizes fetal livers from pregnant mice. Our technique reduces expansion time to 4 days, and generates ~15,000–20,000 MKs per liver. Approximately, 20–50% of these MKs produce structurally dense, high-quality proplatelets. In this review, we outline our method of MK culture and isolation.
Cerebral blood perfusion deficits using dynamic susceptibility contrast MRI with gadolinium chelates in rats with post-ischemic reperfusion without significant dynamic contrast-enhanced MRI-derived vessel permeabilities: A cautionary note

In this study, we quantified perfusion deficits using dynamic susceptibility contrast magnetic resonance imaging (DSC-MRI) with an extravasating contrast agent (CA). We also investigated the efficacy of leakage compensation from CA pre-load in brains from post-ischemic rat models without significant dynamic contrast-enhanced MRI (DCE-MRI)-derived vessel wall permeability. DSC measurements were obtained using fast (0.3 s) echo-planar imaging in both normal rats and rats with transient middle carotid artery occlusion (MCAO) (1-h MCAO, 24-h reperfusion) after successive administrations of gadoterate meglumine (Dotarem) and intravascular superparamagnetic iron oxide nanoparticles (SPION). The relative cerebral blood volume (CBV) and cerebral blood flow (CBF) values acquired using Dotarem were significantly underestimated (~20%) when compared to those acquired using SPION in ipsilesional post-ischemic brain regions. A slight overestimation of relative mean transit time was observed. Areas with underestimated CBV and CBF values from the corresponding error maps encompassed the area of infarcted tissue (apparent diffusion coefficient < 500 μm2/s) and mostly coincided with the area wherein conspicuous longitudinal relaxation time differences were observed pre- vs. post-injection of Dotarem. The DSC measurements with significant pre-load (0.3 mmol·kg-1) of Dotarem displayed minimal perfusion deficits when compared to those determined using the reference intravascular SPION.
Journal of Steroid Biochemistry and Molecular Biology

The vitamin D-modulated transcriptome of highly responsive human cells, such as THP-1 monocytes, comprises more than 500 genes, half of which are primary targets. Recently, we proposed a chromatin model of vitamin D signaling demonstrating that nearly all vitamin D target genes are located within vitamin D-modulated topologically associated domains (TADs). This model is based on genome-wide binding patterns of the vitamin D receptor (VDR), the pioneer transcription factor PU.1, the chromatin organizer CTCF and histone markers of active promoter regions (H3K4me3) and active chromatin (H3K27ac). In addition, time-dependent data on accessible chromatin and mRNA expression are implemented. For the interrogation and in deep inspection of these high-dimensional datasets unsupervised and supervised machine learning algorithms were applied. Unsupervised methods, such as the vector quantization tool K-means and the dimensionality reduction algorithm self-organizing map, generated descriptions of how attributes, such as VDR binding and chromatin accessibility, a ﬀ ect each other as a function of time and/or co-localization within the same genomic region. Supervised algorithms, such as random forests, allowed the data to be classi ﬁ ed into pre-existing categories like persistent ( i.e . constant) and time-dependent ( i.e . transient) VDR binding sites. The relative amounts of these VDR categories in TADs showed to be the main discriminator for sorting the latter into ﬁ ve classes carrying vitamin D target genes involved in distinct biological processes. In conclusion, via the application of machine learning methods we identi ﬁ ed the spatio-temporal VDR binding pattern in TADs as the most critical attribute for speci ﬁ c regulation of vitamin D target genes and the segregation of vitamin D ’ s physiologic function.
Are open and neurotic behaviors related to cognitive behaviors in daily life of older adults?

OBJECTIVE Previous research has shown a positive relationship between Openness and cognitive engagement as well as Neuroticism and cognitive complaints at the between-person level. However, less is known about these associations at the within-person level in daily life. Using daily assessments, the present study examined these associations both at the between-person and within-person level. Knowing the within-person associations is important to provide valuable information for simple preventive and interceptive intervention strategies. METHOD This study sampled 136 healthy older participants (M = 70.45 years; 41.2% male). Open and neurotic behaviors as well as cognitive engagement and complaints were measured every evening over 11 days. RESULTS The results of multilevel models showed a positive association between open behaviors and cognitive engagement at the between-person and within-person level. For neurotic behaviors and cognitive complaints, no association was found at either level of analysis. CONCLUSIONS These findings extend previous research by providing the investigation of the associations between specific naturally occurring behaviors related to personality and cognition in the daily life of older adults at the within-person level. Furthermore, these results may offer some basis for future intervention studies that should test whether a simple intervention aimed at promoting Openness-related behaviors may increase cognitive engagement.
Epigenetic activation of HORMAD1 in basal-like breast cancer: role in Rucaparib sensitivity

Basal-like breast cancer (BLBC) is an aggressive breast cancer subtype with features similar to the basal cells surrounding the mammary ducts. Treatment of patients with BLBC has been challenging due to the lack of well-defined molecular targets. Due to the clinical and pathological similarities of BLBC with BRCA-deficient breast cancers, the effectiveness of Poly (ADP-ribose) polymerase inhibitors (PARPi) has been tested in early phase clinical trials for patients with advanced BLBC, with limited clinical responses. Recently, it was reported that HORMAD1 overexpression sensitizes BLBC to HR-targeting agents by suppressing homologous recombination. Our independent analysis suggests that HORMAD1 is aberrantly overexpressed in about 80% of BLBC, and its expression in normal tissues is restricted to testis. Our experimental data suggests that HORMAD1 overexpression correlates with focal hypomethylation in BLBC. On the other hand, investigation of the Genomics of Drug Sensitivity in Cancer dataset revealed significantly reduced sensitivity of HORMAD1-overexpressing BLBC cell lines to Rucaparib, a commonly used PARPi. To further assess the role of HORMAD1 in PARPi sensitivity, we generated three HORMAD1-overexpressing xenograft models using the HORMAD1-low BLBC cell lines HCC1954, HCC1806, and BT20; we then subjected these xenograft models to Rucaparib treatment. Ectopic expression of HORMAD1 enhances tumor formations in two of these models, and significantly reduces sensitivity to Rucaparib in the HCC1954 model. Taken together, our data suggest that epigenetic activation of HORMAD1 by hypomethylation in BLBC may endow reduced sensitivity to Rucaparib treatment in some tumor models.
Design of 0.14 thz lens integrated on-chip antenna with defected ground structure

In this paper, a 0.14 THz lens integrated on-chip antenna, extensively used in terahertz monolithic integrated circuit (TMIC), is presented. The planar antenna is composed of a double slot radiating element, a microstrip transmission line and a defected ground structure (DGS). Surface-wave losses and back radiation are reduced and a gain of 23.8 dB is obtained by using a λ/4 metallic reflective cavity and an extended hemispherical lens. More than 55% (78GHz) impedance bandwidth is achieved and a relatively low side lobe is gotten by optimizing the parameters of the DGS on the ground of the microstrip line.
Microbial community assembly differs across minerals in a rhizosphere microcosm

Mineral-associated microbes drive many critical soil processes, including mineral weathering, soil aggregation and cycling of mineral-sorbed organic matter. To investigate the interactions between soil minerals and microbes in the rhizosphere, we incubated three types of minerals (ferrihydrite, kaolinite and quartz) and a native soil mineral fraction near roots of a common Californian annual grass, Avena barbata, growing in its resident soil. We followed microbial colonization of these minerals for up to 2.5 months - the plant's lifespan. Bacteria and fungi that colonized mineral surfaces during this experiment differed across mineral types and differed from those in the background soil, implying that microbial colonization was the result of processes in addition to passive movement with water to mineral surfaces. Null model analysis revealed that dispersal limitation was a dominant factor structuring mineral-associated microbial communities for all mineral types. Once bacteria arrived at a mineral surface, capacity for rapid growth appeared important, as ribosomal copy number was significantly correlated with relative enrichment on minerals. Glomeromycota (a phylum associated with arbuscular mycorrhizal fungi) appeared to preferentially associate with ferrihydrite surfaces. The mechanisms enabling the colonization of soil minerals may be foundational in shaping the overall soil microbiome composition and development of persistent organic matter in soils.
Over-the-Air Radiated Testing of Millimeter-Wave Beam-Steerable Devices in a Cost-Effective Measurement Setup

With the severe spectrum congestion of sub-6 GHz cellular systems, large-scale antenna systems in the millimeter-wave (mmWave) bands can potentially meet the high data rate envisioned for fifth generation communications. Performance evaluation of antenna systems is an essential step in the product design and development stage. However, conventional cable conducted test methods are not applicable for mmWave devices. There is a strong need for over-the-air (OTA) radiated methods, where mmWave device performance can be evaluated in a reliable, repeatable, and feasible way in laboratory conditions. In this article, radiated testing methods are reviewed, with a focus on their principle and applicability for beam steerable mmWave devices. To explore the spatial sparsity of mmWave channel profiles, a cost-effective simplified 3D sectored multi-probe anechoic chamber system with an OTA antenna selection scheme is proposed. This setup is suitable for evaluation of beam-steerable devices, including both base station and user equipment devices. The requirements for the test system design are analyzed, including the measurement range, number of OTA antennas, number of active OTA antennas, and amount of channel emulator resource. Finally, several metrics to validate system performance are described for evaluation of mmWave devices.
Economic impact of tolvaptan treatment vs. fluid restriction based on real-world data among hospitalized patients with heart failure and hyponatremia

ABSTRACT Objectives: To estimate the cost difference associated with tolvaptan treatment vs. fluid restriction (FR) among hospitalized patients with heart failure (HF) and hyponatremia (HN) based on a real-world registry of HN patients. Methods: An Excel-based economic model was developed to evaluate the cost impact of tolvaptan treatment vs. FR. Model input for hospital length of stay (LOS) was based on published data from the Hyponatremia Registry (HNR). Based on HNR data, tolvaptan-treated patients had a 2-day (median) shorter LOS compared to FR. Real-world effectiveness of tolvaptan treatment from the HNR was applied to a national sample of inpatients visits from the Premier Hospital database to estimate the potential LOS-related cost difference between tolvaptan treatment and FR. A one-way sensitivity and multivariable Monte Carlo sensitivity analysis were conducted. Results: Economic modeling results of the base-case analysis indicated that among hospitalized patients with HF, the hospital cost per admission, not including HN drug cost, was $3453 lower among patients treated with tolvaptan vs. FR, due to the shorter LOS associated with tolvaptan treatment. At wholesale acquisition cost of $362 per day and an average treatment duration of 3.2 days, the pharmacy cost of tolvaptan treatment per admission was estimated at $1157. Thus, after factoring the decrease in hospital medical costs and increase in pharmacy costs associated with tolvaptan treatment, results indicated a cost-offset opportunity of –$2296 per admission for patients treated with tolvaptan versus FR. Results of the sensitivity analyses were consistent with the base-case analysis. Limitations: The model derives inputs from real-world observational data. No causal relationship can be inferred from this analysis. Conclusions: Based on this economic analysis, tolvaptan treatment vs. FR among hospitalized patients with HF and HN may be associated with lower hospital-related costs, which offset the increase in pharmacy costs associated with tolvaptan treatment.
Evaluation of an Explicit Intervention to Teach Novel Grammatical Forms to Children With Developmental Language Disorder.

Purpose Unlike traditional implicit approaches used to improve grammatical forms used by children with developmental language disorder, explicit instruction aims to make the learner consciously aware of the underlying language pattern. In this study, we compared the efficacy of an explicit approach to an implicit approach when teaching 3 novel grammatical forms varying in linguistic complexity. Method The study included twenty-five 5- to 8-year-old children with developmental language disorder, 13 of whom were randomized to receive an implicit-only (I-O) intervention whereas the remaining 12 participants were randomized to receive a combined explicit-implicit (E-I) intervention to learn 3 novel grammatical forms. On average, participants completed 4.5 teaching sessions for each form across 9 days. Acquisition was assessed during each teaching session. Approximately 9 days posttreatment for each form, participants completed probes to assess maintenance and generalization. Results Analyses revealed a meaningful and statistically significant learning advantage for the E-I group on acquisition, maintenance, and generalization measures when performance was collapsed across the 3 novel targets (p < .02, Φs > 0.60). Significant differences between the groups, with the E-I group outperforming the I-O group, only emerged for 1 of the 3 target forms. However, all effect sizes ranged from medium to large (Φs = 0.25-0.76), and relative risk calculations all exceeded 0, indicating a greater likelihood of learning the target form with E-I instruction than I-O instruction. Conclusions Study findings indicate that, as compared to implicit instruction, children are more likely to acquire, maintain, and generalize novel grammatical forms when taught with explicit instruction. Further research is needed to evaluate the use of explicit instruction when teaching true grammatical forms to children with language impairment.
Anatomical projections of the dorsomedial hypothalamus to the periaqueductal grey and their role in thermoregulation: a cautionary note

The DMH is known to regulate brown adipose tissue (BAT) thermogenesis via projections to sympathetic premotor neurons in the raphe pallidus, but there is evidence that the periaqueductal gray (PAG) is also an important relay in the descending pathways regulating thermogenesis. The anatomical projections from the DMH to the PAG subdivisions and their function are largely elusive, and may differ per anterior–posterior level from bregma. We here aimed to investigate the anatomical projections from the DMH to the PAG along the entire anterior–posterior axis of the PAG, and to study the role of these projections in thermogenesis in Wistar rats. Anterograde channel rhodopsin viral tracing showed that the DMH projects especially to the dorsal and lateral PAG. Retrograde rabies viral tracing confirmed this, but also indicated that the PAG receives a diffuse input from the DMH and adjacent hypothalamic subregions. We aimed to study the role of the identified DMH to PAG projections in thermogenesis in conscious rats by specifically activating them using a combination of canine adenovirus‐2 (CAV2Cre) and Cre‐dependent designer receptor exclusively activated by designer drugs (DREADD) technology. Chemogenetic activation of DMH to PAG projections increased BAT temperature and core body temperature, but we cannot exclude the possibility that at least some thermogenic effects were mediated by adjacent hypothalamic subregions due to difficulties in specifically targeting the DMH and distinct subdivisions of the PAG because of diffuse virus expression. To conclude, our study shows the complexity of the anatomical and functional connection between the hypothalamus and the PAG, and some technical challenges in studying their connection.
Effectiveness and safety of different amifostine regimens: Preliminary results of a phase II multicenter randomized controlled trial.

Objective The radioprotective effects of amifostine remain uncertain in patients with nasopharyngeal carcinoma (NPC), and adverse effects and cost limit generalization of its classical everyday regimen. This phase II multicenter randomized controlled trial aimed to explore whether amifostine could ameliorate the toxicities of NPC patients in the era of intensity-modulated radiotherapy (IMRT), and to compare different regimens of amifostine on effectiveness and safety. Methods Patients with stage I-IVB NPC were involved prospectively from January 1st, 2013. All patients received radical treatment based on IMRT. After a randomization stratified by their stage, these patients were allocated into 3 groups: the group treated without amifostine, the group treated with the everyday regimen of amifostine, and the group treated with the every-other-day regimen. The 3 groups of patients were compared on radiotherapy-related acute toxicities, treatment effects of NPC, and amifostine-related complications. This trial was registered on the clinicaltrials.gov (ID: NCT01762514). Results Until August 31st, 2017, totally 187 patients completed experimental intervention. Only amifostine of everyday regimen appeared to reduce the patient proportion of mucositis (79.1% vs. 96.8%, P=0.002). Hypocalcemia was less common in patients treated without amifostine than in those treated with amifostine (22.6% vs. 53.4% vs. 41.8%, P=0.002). Neither complete remission rates nor the survivals were affected by amifostine. Conclusions Amifostine of everyday regimen could reduce mucositis in NPC patients who received IMRT, though it also had the possibility to cause more hypocalcemia.