Miracle-dz/UniFAR-FTUs huggingface dataset:
Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

Visualizing a response to light Many biological processes depend on detecting and responding to light. The response is often mediated by a structural change in a protein that begins when absorption of a photon causes isomerization of a chromophore bound to the protein. Pande et al. used x-ray pulses emitted by a free electron laser source to conduct time-resolved serial femtosecond crystallography in the time range of 100 fs to 3 ms. This allowed for the real-time tracking of the trans-cis isomerization of the chromophore in photoactive yellow protein and the associated structural changes in the protein. Science, this issue p. 725 The trans-to-cis isomerization of a key chromophore is characterized on ultrafast time scales. A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.
First report of natural infestation of Ovomermis sinensis (Nematoda: Mermithidae) parasitizing fall armyworm Spodoptera sp. (Lepidoptera: Noctuidae) in Himachal Pradesh, India

Spodoptera frugiperda invaded in India at the end of 2018 and has caused severe damage to maize including other crops. Several S. frugiperda naturally parasitized by nematodes were observed in Nauni, Himachal Pradesh, India. The morphological features based on the results of scanning electron microscopy indicated that the nematode belongs to the family Mermithidae. Furthermore, characters discovered that the nematode belongs to Ovomermis sinensis, a known entomoparasitic nematode. Our finding was the first record that S. frugiperda, was naturally parasitized by O. sinensis. The results of this study are of great importance for potential biological control of S. frugiperda by indigenous natural beneficial organisms, i.e., O. sinensis within an integrated pest management system.
Precision Follicular Self-Measurement Using a Pocket-Sized Transabdominal Ultrasound Device

Background: The purpose of this study was to determine the comparability of follicle diameters measured using a pocket-size transabdominal ultrasound (TAUS) device that produces images for self-assessment versus those measured using a conventional transvaginal ultrasound (TVUS) device. The pocket-sized device is fitted with a probe that can be connected to an electronic tablet for patient use and outputs follicle images for patient review.Methods: A prospective study was performed in 25 women (50 follicles) who underwent in vitro fertilization (IVF)/intracytoplasmic sperm injection between November 2019 and March 2020 to treat infertility. Patients were first provided with guidance from a doctor; then, they used the probe attached to the pocket-sized TAUS device to acquire the follicle images. The doctor then measured the follicle diameter using a TVUS device and compared the measurements with those obtained by viewing the images taken by the patient. The transverse cross-sectional follicle diameter measured on transabdominal images was defined as the abdominal transverse (AT) diameter. The sagittal and coronal cross-sectional follicle diameters measured on transvaginal images were defined as the vaginal sagittal (VS) and vaginal coronal (VC) diameters, respectively. The mean values of each parameter and the variance ratio of the difference between the TAUS and TVUS measurements were evaluated.Results: The results showed that the difference between AT-VS in the two imaging types was -0.382 mm (95% CI: -1.097-0.333 mm, P=0.288), whereas the difference between AT-VC was 0.342 mm (95% CI: -0.345-1.029 mm, P=0.322), and that between VS-VC was 0.724 mm (95% CI: 0.152-1.296 mm, P=0.014). The variance ratios for the differences between the TAUS and TVUS measurements and for the differences between the two TVUS cross-sectional measurements were σAT-VS2/σVS-VC2=1.56 and σAT-VC2/σVS-VC2=1.44, respectively.Conclusion(s): Despite the presence of some differences in precision due to differences in the method of imaging when patients performed follicular self-measurement using pocket-sized devices, there was little scattering. Therefore, this method can be used to measure follicle diameter at a precision that presents no issues at the clinical level.Trial Registration: Medical Park Shonan (2019001, 25 October 2019)
Weak-lensing Power Spectrum Reconstruction by Counting Galaxies. I. The ABS Method

We propose an analytical method of blind separation (ABS) of cosmic magnification from the intrinsic fluctuations of galaxy number density in the observed galaxy number density distribution. The ABS method utilizes the different dependences of the signal (cosmic magnification) and contamination (galaxy intrinsic clustering) on galaxy flux to separate the two. It works directly on the measured cross-galaxy angular power spectra between different flux bins. It determines/reconstructs the lensing power spectrum analytically, without assumptions of galaxy intrinsic clustering and cosmology. It is unbiased in the limit of an infinite number of galaxies. In reality, the lensing reconstruction accuracy depends on survey configurations, galaxy biases, and other complexities due to a finite number of galaxies and the resulting shot noise fluctuations in the cross-galaxy power spectra. We estimate its performance (systematic and statistical errors) in various cases. We find that stage IV dark energy surveys such as Square Kilometre Array and Large Synoptic Survey Telescope are capable of reconstructing the lensing power spectrum at and accurately. This lensing reconstruction only requires counting galaxies and is therefore highly complementary to cosmic shear measurement by the same surveys.
Mnemonic prediction errors promote detailed memories

When our experience violates our predictions, it is adaptive to update our knowledge to promote a more accurate representation of the world and facilitate future predictions. Theoretical models propose that these mnemonic prediction errors should be encoded into a distinct memory trace to prevent interference with previous, conflicting memories. We investigated this proposal by repeatedly exposing participants to pairs of sequentially presented objects (A → B), thus evoking expectations. Then, we violated participants’ expectations by replacing the second object in the pairs with a novel object (A → C). The following item memory test required participants to discriminate between identical old items and similar lures, thus testing detailed and distinctive item memory representations. In two experiments, mnemonic prediction errors enhanced item memory: Participants correctly identified more old items as old when those items violated expectations during learning, compared with items that did not violate expectations. This memory enhancement for C items was only observed when participants later showed intact memory for the related A → B pairs, suggesting that strong predictions are required to facilitate memory for violations. Following up on this, a third experiment reduced prediction strength prior to violation and subsequently eliminated the memory advantage of violations. Interestingly, mnemonic prediction errors did not increase gist-based mistakes of identifying old items as similar lures or identifying similar lures as old. Enhanced item memory in the absence of gist-based mistakes suggests that violations enhanced memory for items’ details, which could be mediated via distinct memory traces. Together, these results advance our knowledge of how mnemonic prediction errors promote memory formation.
Estimate of scattering truncation in the cavity attenuated phase shift PMSSA monitor using radiative transfer theory

ABSTRACT The recently developed cavity attenuated phase shift particulate matter single scattering albedo (CAPS PMSSA) monitor has been shown to be fairly accurate and robust for real-time aerosol optical properties measurements. The scattering component of the measurement undergoes a truncation error due to the loss of scattered light from the sample tube in both the forward and backward directions. Previous studies estimated the loss of scattered light typically using the Mie theory for spherical particles, assuming particles are present only on the sampling tube centerline, and without accounting for the effects of sampling tube surface reflection. This study overcomes these limitations by solving the radiative transfer equation in an axisymmetric absorbing and scattering medium using the discrete-ordinates method to estimate the scattering truncation error. The effects of absorption coefficient, scattering coefficient, asymmetry parameter of the scattering phase function, and the reflection coefficient at the sampling tube inner surface were investigated. Under typical conditions of CAPS PMSSA operation of low extinction coefficients below about 5000 Mm−1, the scattering loss remains independent of the absorption and scattering coefficients but is dependent on the scattering phase function and the reflection coefficient of the sampling glass tube inner surface. The proposed method was used to investigate the effects of asymmetry parameter and surface reflection coefficient on truncation for absorbing aerosol particles whose scattering phase function can be well represented by the Henyey-Greenstein approximation. The scattering loss increases with increasing the asymmetry parameter and the surface reflection coefficient. Copyright © 2018 National Research Council Canada
Avocado seed hydrolysate as an alternative growth medium for fungi

Fungi are diverse organisms that inhabit all niches on earth, with great metabolic diversity and various developmental structures. Cultivation of fungi is necessary for their genetic, biochemical, and morphological characterization. Due to their great metabolic capacity, fungi can grow on poorly processed raw materials. That quality has been taken advantage of to formulate inexpensive growth media such as those based on potato. Here, we test the suitability of a growth media consisting of hydrolysates of avocado seeds (ASM), which are by-products of avocado agroindustry, to cultivate six different fungal isolates coming from strawberry plants. We compared the performance of this medium versus PDA and V8, two well-known media among mycologists. We show that ASM is a competitive and suitable medium for fungal growth.
A review of test protocols for the evaluation of teat disinfectants

The prevention of mastitis is the most important part of a mastitis control programme. Postmilking disinfection is considered the most effective procedure for preventing new intramammary infections in dairy herds. This article reviews the different protocols used to evaluate the efficacy of teat disinfectant products. These protocols include experimental challenge, natural exposure and excised teat, along with agar diffusion assays and teat swabbing. The experimental designs, limitations, positive and negative aspects of each protocol were compared and discussed throughout this article.
Construction of biology critical thinking test of high school students

Students must have various abilities, one of which is critical thinking skills. Critical thinking is an ability that is an indicator of successful learning and is directly related to real life. Should carry out the development of critical thinking skills effectively and efficiently in education. Critical thinking skills of students, accurate measurement tools are needed. The measuring instrument is in the form of a test instrument developed through research. Conduct the researched with a quantitative approach by describing the characteristics of the critical thinking test instrument. The research method was the development of a test with the research subjects of class X MIPA students from seven public high schools in Kendal Regency with the criteria of high, medium, and low ranking schools. Developed the test in the form of multiple-choice reasoned with three scoring categories for each item according to the scoring of the polytomous items in the PCM 1-PL model (Partial Credit Model 1 Parameter Logistic). The feasibility test of the critical thinking test instrument was carried out with experts in measurement, assessment, and Biology Learning and was tested empirically on 1118 students. The research data were analyzed using the EXCEL, SPSS 16, QUEST and PARSCALE applications. The results showed that: (1) The test instrument with four categories of scores fit the PCM 1-PL model; (2) the test instrument has a high-reliability value; (3) The test instrument has a right level of difficulty; (4) The test instrument can be used to measure the ability of students in the range of -3.7 to 2.9. The test instrument developed was feasible to be used to measure students' critical thinking skills with three categories of polytomous scoring with the PCM 1-PL model.
Towards Balanced Reciprocity: The Relationship between Landowners and Landless Peasants in the Rural Community

Reciprocity relationships are a necessity in human life. This study aims to describe the various factors that determine the formation of balanced reciprocity in the relationship between land owners and farm laborers. The research's location was determined intentionally in the rural areas of Purbalingga Regency and Banyumas Regency, Central Java Province, Indonesia. This study used a qualitative method with a semi-grounded phenomenological research design. The results showed that a balanced reciprocity relationship was determined by a variety of principal and smoothing factors. The identification results showed that the main determinants include opportunity, benefit, mutual trust, closeness of social relations, motives for reciprocal exchange, openness in communication, willingness to give transactions to accept and return. The array of determinants of smoothing factors is routine contact and communication, empathy, tolerance, length of relationship, regularity of social interactions, network of cooperation, solidarity, transaction ability, mutual control and evaluation. The existence and strength of these two types of determining factors have an important function in the formation of balanced reciprocity among agricultural land owners and farm laborers. Willingness, self-awareness and opportunity are very important to develop to form balanced reciprocity.
Ac Zeeman Force With Ultracold Atoms

Ultracold atom experiments use a gas of neutral atoms with temperatures less than 100 μK above absolute zero and offer unmatched experimental control of quantum states and coherence, which has allowed ultracold atom-based measurements to be some of the most precise to date. While ultracold atom experiments can control almost all atomic degrees of freedom, spin-dependent trapping and spatial manipulation has remained difficult if not inaccessible. We are developing a method of spin-dependent trapping and spatial manipulation for ultracold neutral atoms using the AC Zeeman force produced by a microwave magnetic near-field gradient generated by an atom chip. We measure the AC Zeeman force on ultracold rubidium atoms by observing its effect on the motion of atoms initially in free-fall and on those confined in a trap. We have studied the force as a function of microwave frequency detuning from a hyperfine transition at 6.8 GHz at several magnetic field strengths and have observed its characteristic bipolar and resonant features predicted by two-level dressed atom theory. We find that the force is several times the strength of gravity in our setup, and that it can be targeted to a specific hyperfine transition while leaving other hyperfine states and transitions relatively unaffected. We find that our measurements are reasonably consistent with parameter-free theoretical predictions.
Six solutions for more reliable infant research

Infant research is often underpowered, undermining the robustness and replicability of our findings. Improving the reliability of infant measures offers a solution for increasing statistical power independent of sample size. Here, we discuss two senses of the term reliability in the context of infant research: reliable (large) effects and reliable measures. We examine the circumstances under which effects are strongest and measures are most reliable, and provide simulations to illustrate the relationship between effect size, measurement reliability, and statistical power. We then present six concrete solutions for improving measurement in infant research: (1) routinely estimating and reporting the effect size and measurement reliability of infant tasks, (2) selecting the best measurement tool, (3) developing better infant paradigms, (4) collecting more data points per infant, (5) excluding unreliable data from analysis, and (6) conducting more sophisticated data analyses. Deeper consideration of measurement in infant research will improve our ability to study infant development.
Determination of factors affecting competitiveness through technical and economic analysis of dairy cattle enterprises in Balıkesir province

: In this study, technical and economic analysis of dairy cattle enterprises in Balıkesir province were carried out. The factors which affect the competitiveness of enterprises and are important in terms of the continuity of production were determined. The stratified sampling method was used to determine the sample, and the study material was two-year (2017–2018) data obtained from 147 enterprises. In addition to the economic analysis of the data obtained, factors affecting unit profit in enterprises were estimated using the multiple linear regression model. The cost elements in total enterprises in Balıkesir province in 2017–2018 include feed expenses (47.90%-47.29%), livestock depreciation (16.64%-16.13%), labor expenses (13.84%-14.30%), veterinary health expenses (4.03%-4.50%), fuel transportation expenses (3.43%-4.15%), building equipment depreciation (3.37%-3.64%), and other expense items. A distinct difference was observed between scales in terms of profit and loss states of the enterprises in the study, with an increase in the profitability level from small toward large scale enterprise. The small-scale enterprises, in particular, are at a loss. The most important determinant of competitiveness in the study is the region’s development level, where the enterprises are established in the borders of Balıkesir province. Additionally, among the technical parameters, the calving interval and the reduction of the disease rate have a positive effect on the competitiveness of the enterprises. Therefore, improving the financial structure of the enterprises and boosting the rate of technology utilization while simultaneously increasing enterprise scales will contribute positively to competitiveness.
Impacts of disturbance on the terrestrial carbon budget of North America

Because it is an important regulator of terrestrial carbon cycling in North America, extensive research on natural and human disturbances has been carried out as part of the North American Carbon Program and the CarboNA project. A synthesis of various components of this research was carried out, and the results are presented in the papers contained in this special section. While the synthesis primarily focused on the impacts of fire, insects/disease, and harvesting on terrestrial carbon cycling in forests, several groups focused on impacts of disturbance on woody encroachment in western U.S. dry lands and on soil carbon present in northern high‐latitude regions. Here, we present a summary of the results from these papers, along with the findings and recommendations from the disturbance synthesis.
Antioxidant and hepatoprotective property of squalene for counteracting the oxidative damage induced by methotrex- ate in experimental rats

Methotrexate (MTX), an antifolate drug, is extensively prescribed for patients suﬀering from diseases like cancer, psoriasis, neoplasms, and rheumatoid arthritis. Despite its eﬀectiveness, MTX sometimes ﬁnds limited application because its undesirable side eﬀects, including hepatic or renal impairment, bone marrow toxicity and gastrointestinal mucosal injury. Squalene, a highly unsaturated isoprenoid compound, isolated from shark liver oil has great potential in neutralizing the damaging eﬀects triggered by free radicals. Therefore, in this study, the protective role of dietary squalene supplementation on oxidative stress induced by methotrexate in experimental rats was evaluated. A signiﬁcant reduction was displayed in the activities of catalase (CAT) and superoxide dismutase (SOD) in MTX-intoxicated groups compared to other groups. Similarly, the activities of glutathione dependant enzymes (GPx and GST) and reduced glutathione (GSH) in MTX-induced groups were shown to be lower compared to the untreated control. Increased LPO (lipid peroxide) level was found in MTX-intoxicated groups compared to other groups. In addition, alterations in the levels of liver marker enzymes like AST, ALP, ALT, and LDH were noticed in MTX intoxicated groups compared to other groups. Biochemical results were conﬁrmed by the histopathological examination of liver sections. In conclusion, the result obtained in the present study proposes that squalene exerts antioxidant activity and is capable of ameliorating oxidative stress and liver injury induced by MTX.
Effect of Screen-Time on Sleep Pattern and Dietary Habits among College-Going Students in COVID-19 Pandemic

Background: Optimum and good quality of sleep are pertinent to the health and equilibrium of biological functions. Increased use of electronic gadgets for academics and social interactions during the COVID-19 pandemic has extended the screen time of students, affecting sleep and eating patterns. Aim & Objective: To study the association of extended screen time on sleep pattern and calorie intake among college students during the COVID-19 pandemic. Settings and Design: Observational study was conducted using ‘Google forms’ to collect data on sleep and food intake among 60 college-going students. Methods and Material: Google form composed of questions related to demographic, anthropometry, screen time, sleep quality (PSQI) & dietary pattern (food frequency questionnaire) and tied to written consent was sent via WhatsApp to college students. Statistical analysis used: Data were grouped based on the screen time >10 hrs and </=10 hrs/day. Independent “t” test, Chi-square test and Mann Whitney test were used to compare the sleep domains scores and calorie intake. Results: With an average screen time of 10.9 hrs, 38% of students were using the screen maximally during the night. Poor Sleep Quality was (PSQI Score>5) observed in 80% of the college students, with 46.6% having a sleep of <5 hrs/day. Students' calorie intake was ten times the recommended daily requirement during the stay at home but was negatively related to screen-time, though non-significant. Conclusions: The study concludes that average screen time of students of age group 18-24 years have increased during night under the lockdown. This extended viewing in night has shifted the sleep circadian cycle to morning hours, with daytime sleepiness and poor sleep quality. The high calorie intake was also observed in students during lockdown though no correlation was established with the screen time and sleep quality.