Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuronal sequences during theta rely on behavior-dependent spatial maps

Navigation through space involves learning and representing relationships between past, current, and future locations. In mammals, this might rely on the hippocampal theta phase code, where in each cycle of the theta oscillation, spatial representations provided by neuronal sequences start behind the animal’s true location and then sweep forward. However, the exact relationship between theta phase, represented position and true location remains unclear and even paradoxical. Here, we formalize previous notions of ‘spatial’ or ‘temporal’ theta sweeps that have appeared in the literature. We analyze single-cell and population variables in unit recordings from rat CA1 place cells and compare them to model simulations based on each of these schemes. We show that neither spatial nor temporal sweeps quantitatively accounts for how all relevant variables change with running speed. To reconcile these schemes with our observations, we introduce ‘behavior-dependent’ sweeps, in which theta sweep length and place field properties, such as size and phase precession, vary across the environment depending on the running speed characteristic of each location. These behavior-dependent spatial maps provide a structured heterogeneity that is essential for understanding the hippocampal code.
MUC1-C dictates neuroendocrine lineage specification in pancreatic ductal adenocarcinomas

Abstract Pancreatic ductal adenocarcinomas (PDAC) and poorly differentiated pancreatic neuroendocrine (NE) carcinomas are KRAS mutant malignancies with a potential common cell of origin. PDAC ductal, but not NE, lineage traits have been associated with cell-intrinsic activation of interferon (IFN) pathways. The present studies demonstrate that the MUC1 C-terminal subunit (MUC1-C), which evolved to protect mammalian epithelia from loss of homeostasis, is aberrantly overexpressed in KRAS mutant PDAC tumors and cell lines. We show that MUC1-C is necessary for activation of the type I and II IFN pathways and for expression of the Yamanaka OCT4, SOX2, KLF4 and MYC (OSKM) pluripotency factors. Our results demonstrate that MUC1-C integrates IFN signaling and pluripotency with NE dedifferentiation by forming a complex with MYC and driving the (i) achaete-scute homolog 1 and BRN2/POU3F2 neural, and (ii) NOTCH1/2 stemness transcription factors. Of translational relevance, targeting MUC1-C genetically and pharmacologically in PDAC cells (i) suppresses OSKM, NE dedifferentiation and NOTCH1/2, and (ii) inhibits self-renewal capacity and tumorigenicity. In PDAC tumors, we show that MUC1 significantly associates with activation of IFN signaling, MYC and NOTCH, and that upregulation of the MUC1-C → MYC pathway confers a poor prognosis. These findings indicate that MUC1-C dictates PDAC NE lineage specification and is a potential target for the treatment of recalcitrant pancreatic carcinomas with NE dedifferentiation.
Birthweight and subsequent risk for thyroid and autoimmune conditions in postmenopausal women

Abstract The objective of this study was to determine the association between birthweight and risk of thyroid and autoimmune conditions in a large sample of postmenopausal women. Baseline data from the Women’s Health Initiative (n = 80,806) were used to examine the associations between birthweight category (<6 lbs., 6–7 lbs. 15 oz, 8–9 lbs. 15 oz, and ≥10 lbs.) and prevalent thyroid (underactive and overactive thyroid and goiter) and autoimmune (lupus, rheumatoid arthritis (RA), multiple sclerosis, ulcerative colitis/Crohn’s disease) conditions. Follow-up questionnaire data were used to examine the associations between birthweight and incident underactive and overactive thyroid, lupus, and RA. Logistic and Cox proportional hazards regression models were used to estimate crude and adjusted odds (OR) and hazards ratios (HR), respectively. Overall, women born weighing ≥10 lbs. had an increased risk for underactive thyroid [OR 1.14 (95% CI 1.02, 1.28)] and incident lupus [HR 1.51 (95% CI 1.12, 2.03)] and a decreased risk for overactive thyroid [OR 0.67 (95% CI 0.50, 0.92)] compared to women born weighing 6–7.99 lbs. , after adjustment for adult BMI, demographic variables, and lifestyle factors. Further, women born weighing <6 lbs. were at increased risk for underactive thyroid [OR 1.13 (95% CI 1.04, 1.22)]. Birthweight was not associated with other thyroid or autoimmune disorders. High birthweight was associated with later-life thyroid and autoimmune conditions while low birthweight was associated with underactive thyroid. Preconception and prenatal interventions aimed at reducing the risk of both high and low birthweights may reduce the burden of later-life thyroid and autoimmune conditions.
Passive Sensing of Preteens’ Smartphone Use: An Adolescent Brain Cognitive Development (ABCD) Cohort Substudy

Background Concerns abound regarding childhood smartphone use, but studies to date have largely relied on self-reported screen use. Self-reporting of screen use is known to be misreported by pediatric samples and their parents, limiting the accurate determination of the impact of screen use on social, emotional, and cognitive development. Thus, a more passive, objective measurement of smartphone screen use among children is needed. Objective This study aims to passively sense smartphone screen use by time and types of apps used in a pilot sample of children and to assess the feasibility of passive sensing in a larger longitudinal sample. Methods The Adolescent Brain Cognitive Development (ABCD) study used passive, objective phone app methods for assessing smartphone screen use over 4 weeks in 2019-2020 in a subsample of 67 participants (aged 11-12 years; 31/67, 46% female; 23/67, 34% White). Children and their parents both reported average smartphone screen use before and after the study period, and they completed a questionnaire regarding the acceptability of the study protocol. Descriptive statistics for smartphone screen use, app use, and protocol feasibility and acceptability were reviewed. Analyses of variance were run to assess differences in categorical app use by demographics. Self-report and parent report were correlated with passive sensing data. Results Self-report of smartphone screen use was partly consistent with objective measurement (r=0.49), although objective data indicated that children used their phones more than they reported. Passive sensing revealed the most common types of apps used were for streaming (mean 1 hour 57 minutes per day, SD 1 hour 32 minutes), communication (mean 48 minutes per day, SD 1 hour 17 minutes), gaming (mean 41 minutes per day, SD 41 minutes), and social media (mean 36 minutes per day, SD 1 hour 7 minutes). Passive sensing of smartphone screen use was generally acceptable to children (43/62, 69%) and parents (53/62, 85%). Conclusions The results of passive, objective sensing suggest that children use their phones more than they self-report. Therefore, use of more robust methods for objective data collection is necessary and feasible in pediatric samples. These data may then more accurately reflect the impact of smartphone screen use on behavioral and emotional functioning. Accordingly, the ABCD study is implementing a passive sensing protocol in the full ABCD cohort. Taken together, passive assessment with a phone app provided objective, low-burden, novel, informative data about preteen smartphone screen use.
Telephone-delivered Interpersonal Psychotherapy: a systematic review

Abstract Background The aim of this paper is to review evidence on Interpersonal Psychotherapy (IPT) administered via telephone (IPT-T). Methods We conducted a systematic review of studies published between January 1, 1990 and June 30, 2020, assessing the efficacy of IPT administered by phone, using PubMed. Results Originally, we found 60 papers; the final selection led to 13 papers. Six studies were performed using a randomized clinical trial methodology (6/13, 46.2%), three were prospective open-label not randomized studies (3/13, 15.7%), three were pilot studies (3/13, 23.1%), and one was a feasibility/acceptance study (1/13, 7.7%). The number of subjects included in the studies ranged between 14 and 442 (mean: 140.0 ± 124.9), for a total of 1850 patients. The mean age of the enrolled subjects was 47.8 ± 9.3 years (range: 27.4-70.4). Thirty-four different instruments were utilized. Qualitative synthesis was conducted only on randomized controlled trials (RCTs), namely on six studies. RCTs were almost all of good quality (mean score/standard deviation of the RCT-Psychotherapy Quality Rating Scale omnibus rating: 5.6 ± 1.2 points; range: 3-7). Conclusions IPT-T showed response rates similar to IPT administered in the usual way. Results are limited by small samples sizes, selection bias of the less severe depressed patients, and the heterogeneity of rating scales.
Analysis of Meat Consumption Pattern in Ogbomoso North Local Government Area, Oyo State, Nigeria

The increasing awareness of the benefits of more nutritious, healthier and safer food products by consumers plays a vital role in the recent changes experienced in the food production chain, and meat products are no exception to this. The study investigated consumption pattern of meat in Ogbomoso North Local Government Area, Oyo State, Nigeria. Primary data for the study were obtained from 120 respondents with the use of structured questionnaire analysed using descriptive statistics and inferential statistics. According to the study, chicken, turkey and beef with percentage frequencies 96.7%, 81.7% and 76.8% respectively were the most consumed meat types, while quail, rabbit and guinea fowl with percentage frequencies 6.7%, 7.5% and 12.5% respectively were the least consumed meat types. Also, income of the respondent with t-value 41.08 and a positively signed coefficient at 1% level of significance was found to have a direct effect on the monthly expenditure on preferred meat type. The study recommend there should be awareness on the nutritional benefits of consuming meats of low saturated fats and calorie contents such as rabbit, quail and guinea fowl and also to teach them how to raise these animals domestically.
Investigating the Impact of Various Partial Diacritization Schemes on Arabic-English Statistical Machine Translation

Most diacritics in Arabic represent short vowels. In Arabic orthography, such diacritics are considered optional. The absence of these diacritics naturally leads to significant word ambiguity to top the inherent ambiguity present in fully diacritized words. Word ambiguity is a significant impediment for machine translation. Despite the ambiguity presented by lack of diacritization, context helps ameliorate the situation. Identifying the appropriate amount of diacritic restoration to reduce word sense ambiguity in the context of machine translation is the object of this paper. Diacritic marks help reduce the number of possible lexical word choices assigned to a source word which leads to better quality translated sentences. We investigate a variety of (linguistically motivated) partial diacritization schemes that preserve some of the semantics that in essence complement the implicit contextual information present in the sentences. We also study the effect of training data size and report results on three standard test sets that represent a combination of different genres. The results show statistically significant improvements for some schemes compared to two baselines: text with no diacritics (the typical writing system adopted for Arabic) and text that is fully diacritized.
Model-Based Approach for Optimizing Ceftobiprole Dosage in Pediatric Patients

Ceftobiprole is an advanced-generation cephalosporin for intravenous administration with activity against Gram-positive and Gram-negative organisms. A population pharmacokinetic (PK) model characterizing the disposition of ceftobiprole in plasma using data from patients in three pediatric studies was developed. Model-based simulations were subsequently performed to assist in dose optimization for the treatment of pediatric patients with hospital-acquired or community-acquired pneumonia. ABSTRACT Ceftobiprole is an advanced-generation cephalosporin for intravenous administration with activity against Gram-positive and Gram-negative organisms. A population pharmacokinetic (PK) model characterizing the disposition of ceftobiprole in plasma using data from patients in three pediatric studies was developed. Model-based simulations were subsequently performed to assist in dose optimization for the treatment of pediatric patients with hospital-acquired or community-acquired pneumonia. The population PK data set comprised 518 ceftobiprole plasma concentrations from 107 patients from 0 (birth) to 17 years of age. Ceftobiprole PK was well described by a three-compartment model with linear elimination. Ceftobiprole clearance was modeled as a function of glomerular filtration rate; other PK parameters were scaled to body weight. The final population PK model provided a robust and reliable description of the PK of ceftobiprole in the pediatric study population. Model-based simulations using the final model suggested that a ceftobiprole dose of 15 mg/kg of body weight infused over 2 h and administered every 12 h in neonates and infants <3 months of age or every 8 h in older pediatric patients would result in a ceftobiprole exposure consistent with that in adults and good pharmacokinetic-pharmacodynamic target attainment. The dose should be reduced to 10 mg/kg every 12 h in neonates and infants <3 months of age who weigh <4 kg to avoid high exposures. Extended intervals and reduced doses may be required for pediatric patients older than 3 months of age with renal impairment.
Cytokinin Inhibits Fungal Development and Virulence by Targeting the Cytoskeleton and Cellular Trafficking

Cytokinins (CKs), important plant growth/developmental hormones, have previously been associated with host disease resistance. Here, we demonstrate that CK directly inhibits the growth, development, and virulence of B. cinerea (Bc) and many additional phytopathogenic fungi. ABSTRACT Cytokinin (CK) is an important plant developmental regulator, having activities in many aspects of plant life and response to the environment. CKs are involved in diverse processes in the plant, including stem cell maintenance, vascular differentiation, growth and branching of roots and shoots, leaf senescence, nutrient balance, and stress tolerance. In some cases, phytopathogens secrete CKs. It has been suggested that to achieve pathogenesis in the host, CK-secreting biotrophs manipulate CK signaling to regulate the host cell cycle and nutrient allocation. CK is known to induce host plant resistance to several classes of phytopathogens from a few works, with induced host immunity via salicylic acid signaling suggested to be the prevalent mechanism for this host resistance. Here, we show that CK directly inhibits the growth, development, and virulence of fungal phytopathogens. Focusing on Botrytis cinerea (Bc), we demonstrate that various aspects of fungal development can be reversibly inhibited by CK. We also found that CK affects both budding and fission yeast in a similar manner. Investigating the mechanism by which CK influences fungal development, we conducted RNA next-generation sequencing (RNA-NGS) on mock- and CK-treated B. cinerea samples, finding that CK alters the cell cycle, cytoskeleton, and endocytosis. Cell biology experiments demonstrated that CK affects cytoskeleton components and cellular trafficking in Bc, lowering endocytic rates and endomembrane compartment sizes, likely leading to reduced growth rates and arrested developmental programs. Mutant analyses in yeast confirmed that the endocytic pathway is altered by CK. Our work uncovers a remarkably conserved role for a plant growth hormone in fungal biology, suggesting that pathogen-host interactions resulted in fascinating molecular adaptations on fundamental processes in eukaryotic biology. IMPORTANCE Cytokinins (CKs), important plant growth/developmental hormones, have previously been associated with host disease resistance. Here, we demonstrate that CK directly inhibits the growth, development, and virulence of B. cinerea (Bc) and many additional phytopathogenic fungi. Molecular and cellular analyses revealed that CK is not toxic to Bc, but rather, Bc likely recognizes CK and responds to it, resulting in cell cycle and individual cell growth retardation, via downregulation of cytoskeletal components and endocytic trafficking. Mutant analyses in yeast confirmed that the endocytic pathway is a CK target. Our work demonstrates a conserved role for CK in yeast and fungal biology, suggesting that pathogen-host interactions may cause molecular adaptations in fundamental processes in eukaryotic biology.
Understanding Habitat Use and Activity Patterns of Ornate Box Turtle (Terrapene ornata) in Eastern New Mexico

Abstract. The ornate box turtle (Terrapene ornata) is a terrestrial Emydid, listed as near threatened by the International Union for Conservation of Nature Redlist due to habitat destruction, degradation, habitat fragmentation, commercial harvest, and road mortality. Terrapene ornata is secretive, which can pose a challenge to conducting systematic surveys and assessing species status. Studies on the species' biology have relied on opportunistic encounters on the road and the use of radiotelemetry. The objective of this study was to assess the feasibility of using transect line surveys in single season occupancy surveys for T. ornata in Roosevelt County, New Mexico. We further used radiotelemetry to link turtle activity patterns with environmental conditions to aid in understanding detectability of the species. Our occupancy model showed the detection probability to be influenced by individual observers and the time of day. We found T. ornata to most likely occupy habitats with less dense ground cover and avoid highly altered habitats (i.e., cultivated fields). Radiotelemetry further revealed the effect humidity, time of day, and temperature on turtle activity patterns. The lowest activity occurred between 1200–1700 h, whereas peak activity occurred in early morning hours (0600–0900 h). The peak activity occurred between ∼10–25 C and was promoted by higher humidity. Our study represents the first attempt at using transect line surveys for occupancy modeling framework for the ornate box turtles. We suggest that future studies on box turtle occupancy focus on finer scale habitat assessment that would also include vegetation, invertebrate, and small mammal surveys.
Assessing the Impacts of Prescribed Fire and Bison Disturbance on Birds Using Bioacoustic Recorders

Abstract. Grassland bird responses to grazing and prescribed fire are species-specific and are primarily known from systems with cattle as the predominant grazer. There is less knowledge of how grazing by bison impacts grassland birds, especially in sites restored and reconstructed from row-crop agriculture. Working at a tallgrass prairie site consisting of restored and remnant prairie in the years following bison reintroduction and ongoing prescribed burning, we assessed overall species richness and the relative detection frequency of five focal species (Grasshopper Sparrow, Henslow's Sparrow, Dickcissel, Eastern Meadowlark, and Brown-headed Cowbird). We used stationary bioacoustics recorders to record the soundscape during the summer breeding season in areas with and without bison from 2016 to 2018. Species richness and the detection frequencies of our focal species were not influenced by bison disturbance. Grasshopper Sparrow and Dickcissel detection frequency increased slightly in response to prescribed fire, whereas Henslow's Sparrow detection frequency decreased. Time since sites were restored was a predominant factor that influenced the variation in detection frequency of Henslow's Sparrows and Eastern Meadowlarks, likely due to vegetation differences in restored versus remnant sites and each species' vegetation structure preferences. Brown-headed Cowbird detection frequency was unaffected by bison presence, prescribed fire, or time since restoration, but varied among sampling years. Our focal species showed no response to bison disturbance 4 y after the bison reintroduction. This suggests there could be a time-lag for a response or that these species will not respond to the bison reintroduction at this study site.
A Trophic Cascade Following the Introduction of an Omnivorous Fish, Dorosoma cepedianum, in a Mid-continental Reservoir (Mozingo Studies IV)

Abstract. Mozingo Lake, a reservoir in the mid-continental United States, was sampled 63 times between January 1999 and October 2015. Prior to 2005, phytoplankton biovolume was largely composed of Cryptomonas and cyanobacteria (mostly Aphanizomenon); these taxa correlated with the abundance of Daphnia and juvenile copepods, and were also influenced by competition between cyanobacteria and bacillariophytes. These relationships suggest the zooplankton community was primarily controlled by bottom-up processes during this time. In 2005, gizzard shad (Dorosoma cepedianum) first appeared in the lake, coinciding with the first spined and helmeted forms of Daphnia as well as their decline from 39% to 3% of zooplankton; the relative abundance of juvenile copepods increased concurrently. By 2007 phytoplankton biovolume had decreased by 88%. Although all phytoplankton phyla declined in absolute abundance, some were more heavily impacted. The relative abundance of Aphanizomenon declined from 50% to 6% of the phytoplankton biovolume; Cryptomonas remained common, but bacillariophytes became codominant. Despite the steep decline in phytoplankton biovolume, several important trophic interactions did not change: phytoplankton biovolume continued to control juvenile copepods, and competition continued between cyanobacteria and bacillariophytes. Although juvenile copepods continued to compete with Daphnia, the scarcity of the latter allowed a relative expansion of juvenile copepods and bacillariophytes. Because very few of the standard parameters correlated with phytoplankton, it seems likely that most of the changes were caused by the introduction of gizzard shad, which is an intense consumer of cyanobacteria and Daphnia. Gizzard shad likely initiated a trophic cascade both directly (through consumption) and indirectly (by shifting competition). Although other factors may have played a role, it seems clear that the introduction of gizzard shad can cause dramatic changes in both the zooplankton and phytoplankton communities by altering species relationships in top-down, bottom-up, as well as lateral control processes.
Exploring the Experiences of Student Volunteer and Student Volunteer Chair Communities at Academic Conferences

We report on an interview study with two groups, student volunteers (SV) and student volunteer chairs (SVC), to explore their experiences in contributing to an academic conference. We identified themes regarding their behaviors and perceptions when communicating with each other through an open coding approach. The analysis of the findings reveals that communication issues exist between SV and SVC. While SV faced challenges approaching SVC, SVC had experienced difficulties in finding the right SV to ask for assistance in the tasks. We also found that the information provided by SVC was not sufficient for SV to perform the assigned tasks. Similarly, SVC had a similar issue where they received limited information from former SVC. We present design implications that enable both SV and SVC to share their availability, preferences, and prior knowledge of potential tasks with each other. This is the first study that reports design opportunities to support SV and SVC.