Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct mode of action of a highly stable, engineered phage lysin killing Gram-negative bacteria

ABSTRACT Therapeutic options to treat bacterial infections caused by Gram-negative pathogens are limited due to the spread of multidrug resistance. Protein engineering of phage-derived lysins can play a key role in the search for new antimicrobial compounds targeting Gram-negative pathogens. A previous high-throughput screen of a combinatorial lysin library identified lysin 1D10 active against Acinetobacter baumannii under elevated human serum concentrations. The engineered lysin consists of four modules: cecropin A, a linker, cell wall-binding domain, and an enzymatic active domain. Using time-lapse microscopy, we show that 1D10 has a distinct antibacterial mode of action resulting in local cell wall bulging at the septum instead of cell-wide lysis, as observed for previously reported engineered lysins that target Gram-negative bacteria. Our results indicate that the activity of 1D10 relies on the antibacterial activity of both cecropin A (CecA) and the enzymatically active domain. Based on a truncation analysis, the role of each of the four modules of 1D10 was dissected. We further compared the antibacterial spectrum, thermostability, and cytotoxicity of cecropin A alone and lysin 1D10. Both lysin 1D10 and CecA are most active against A. baumannii and are not cytotoxic toward human keratinocytes. Lysin 1D10 unfolds at 57°C and has a remarkable refolding capacity, as it regains its activity even after exposure to 90°C and sterilization conditions, whereas CecA is inactivated at 70°C. Overall, the present study shows that an improved understanding of the killing mechanism and the protein properties will further support lysin engineering designs in the future. IMPORTANCE Engineered lysins are considered as highly promising alternatives for antibiotics. Our previous screening study using VersaTile technology identified 1D10 as a possible lead compound with activity against Acinetobacter baumannii strains under elevated human serum concentrations. In this manuscript, we reveal an unexpected mode of action and exceptional thermoresistance for lysin 1D10. Our findings shed new light on the development of engineered lysins, providing valuable insights for future research in this field. Engineered lysins are considered as highly promising alternatives for antibiotics. Our previous screening study using VersaTile technology identified 1D10 as a possible lead compound with activity against Acinetobacter baumannii strains under elevated human serum concentrations. In this manuscript, we reveal an unexpected mode of action and exceptional thermoresistance for lysin 1D10. Our findings shed new light on the development of engineered lysins, providing valuable insights for future research in this field.
MalPatch: Evading DNN-Based Malware Detection With Adversarial Patches

Static analysis is a crucial protection layer that enables modern antivirus systems to address the rampant proliferation of malware. These systems are increasingly relying on deep neural networks (DNNs) to automatically extract reliable features and achieve outstanding detection accuracy. Since DNNs are known to be vulnerable to adversarial examples, several studies have proposed practical evasion attacks to generate adversarial perturbations that can evade malware detectors. These attacks, however, require specific designs for the given input sample, prohibiting them from large-scale deployment. Therefore, it is more practical to generate sample-agnostic perturbations that do not involve recalculations regardless of the input malware sample. To this end, we leverage an adversarial patch attack, which is a special type of adversarial attack that dose not know the sample being modified during the attack construction process. In particular, we propose a new adversarial attack against malware detection systems called MalPatch. It locates the nonfunctional part of malware for adversarial patch injection to protect its executability while generating adversarial examples based on different strategies. The generated patch can be injected into any malware sample, fooling the detector into classifying it as benign. Experimental results demonstrate that MalPatch is effective under different attack settings. In the white-box setting, MalPatch achieves 69%-78% success rates against DNN detectors based on raw byte features and 47%-96% success rates against four grayscale detectors based on image features. In the black-box setting, the success rates of MalPatch against the same models reach 54%-74% and 27%-42%, respectively. We conclude by discussing several of its potential countermeasures and the generality of our approach.
Sm-Nd age and Sr, Nd isotopic characteristics of the Fanshan potassic alkaline ultramafite-syenite complex in Hebei province, China.

The intrusive complex in the Fanshan, Hebei province, China, consisting of layered patassic alkaline ultramafite and alkaline syenite, is know in the world for its containing large magnetite apatite deposits, and the rocks and deposits have been investigated and a lot of data have been accumulated over the past twenty years. However, their formation timing is still in dispute. Most geologists consider that the rocks and deposits in the Fanshan intrusive complex originated in Triassic Period between 250Ma and 200Ma, but some believe that they were formed in Permian Period. Sm Nd dating of the Fanshan intrusive complex has been performed, and its age have been obtained. The Sm Nd isochron age of four mineral samples and two whole rock samples from the Fanshan intrusive complex is 243.4±9.7Ma with I Nd =0.512045, e Nd ( t )=-5.4, and the Sm Nd isochron age of four mineral samples and seven whole rock samples from the Fanshan intrusive complex is 239±19Ma with I Nd =0.512055, e Nd ( t )=-5.3. These age data indicate that emplacement of the Fanshan complex started at early Triassic period. However, the Rb Sr isochron age in the Fanshan complex is 218±8Ma with I Sr =0.70554,e Sr =18.4, suggesting possibly that the Fanshan complex was solidified completely in the middle Triassic Period. The Sr, Nd isotope fact of the Fanshan complex above shows that the Fanshan complex was derived from enriched mantle materials.
Effect of Different Levels of Hesperetin on the Quality of Rooster Semen

The study examined the impact of varying concentrations of hesperetin on the cryopreservation of rooster sperm. Sperm were diluted with a Lake Extender containing (0, 15, 20, 25, and 30) μM hesperetin. After a 30-second freeze-thaw operation at 37 °C, membrane integrity, sperm motility characteristics, aberrant morphology, apoptotic status, and mitochondrial activity were assessed. The concentration of 25 μM hesperetin observed the highest values ( P < 0.01) were (64.26 %, 30.44 %, 35.88 mm/s, 21.77 mm/s, 61.08 mm/s, 35.66%, 61.14%, 16.23 Hz, 61.71%, 61.71%, and 61.33%) for (Total motility, progressive motility, average velocity path, curved velocity, straight-line velocity, linearity, straightness, beat cross frequency, membrane integrity, mitochondrial activity, and viability, respectively). In contrast, it recorded the lowest values (3.94mm, 13.67%, 13.30%, and 25.37%) for lateral head displacement amplitude, total abnormality, apoptotic sperm, and dead sperm, respectively. It may be concluded that adding 25 μM hesperetin is an effective method for preserving the quality of cryopreserved rooster sperm.
Rubidium-strontium geochronology of the Oaxaca and Acatlan metamorphic areas of southern Mexico

A Rb-Sr study was carried out on crystalline basement rocks from two small separate areas of southern Mexico: Oaxaca area and the Acatlan area. The Oaxaca area consists mainly of orthogneisses and paragneisses of amphibolite to granulite grade metamorphism as well as granitic intrusives. In the present study the following dates and initial /sup 87/Sr//sup 86/Sr rates (Sr/sub 0/) were obtained from rocks of this area: El Cortijo gneisses 341 +/- 61 my, Sr/sub 0/ 0.7226 +/- 0.0027; Ojo de Agua pegmatite 975 +/- 25 my, assumed Sr/sub 0/ 0.710; El Catrin gneisses 1500 +/- 230 my, Sr/sub 0/ 0.7026 +/- 0.0005; Suchilquitongo granite 272 +/- 8 my, Sr/sup 0/ 0.7047 +/- 0.0005; Laachila marble 901 +/- 24 my, Sr/sub 0/ 0.7062 +/- 0.0007; Laachila granitic dike 236 +/- 5 my, Sr/sub 0/ 0.8477 +/- 0.0009. The Acatlan area consists typically of greenschist facies metasedimentary rocks with similar structural and metamorphic characteristics through the area. In the present study, muscovite, biotite and whole rock data points from the typical Acatlan schists collected at different locations within the Acatlan Complex define two different linear arrays from which an age of 481 +/- 9 my, and two Sr/sub 0/ intercepts of 0.7075more » +/- 0.0008 and 0.7112 +/- 0.0006 (95% confidence level) are obtained. The same date is obtained for 18 samples of the Piaxtla augen schist 480 +/- 84 my. Other dates obtained are: Caltepec granitic rocks 269 +/- 21 my, Sr/sub 0/ 0.7056 +/- 0.0004; Tepejillo intrusive bodies 207 +/- 10 my, Sr/sub 0/ 0.7037 +/- 0.0003 and Tepejillo pegmatite 173 +/- 0.3 my, Sr/sub 0/ 0.7044 +/- 0.0002. The tectonic histories of the Oaxaca and Acatlan areas are substantially different and have been unrelated at least until Late Paleozoic times. « less
Patellar Tendon Reconstruction Using Tibialis Posterior Allograft for Treatment of Patellar Tendon Rupture After Bone-Patellar Tendon-Bone Anterior Cruciate Ligament Reconstruction

Background: Bone-patellar tendon-bone (BPTB) autografts are often used to treat anterior cruciate ligament (ACL) tears in young, highly active patients. These grafts are robust and provide adequate stability, allowing for return to sport and optimal functional outcomes in athletes. Patellar tendon rupture following BPTB ACL reconstruction is rare and can be difficult to treat. Case Report: A 19-year-old collegiate wrestler injured his left knee during a match. On evaluation 7 days after the injury, he was foundtohaveincreasedanteriortranslationofthetibiaonLachmantestingandanabnormalpivotshift.Magneticresonanceimag-ing demonstrated a complete tear of the ACL, and he successfully underwent a BPTB ACL reconstruction without complication. He progressed appropriately in the acute postoperative period. Six weeks after his index surgery, the patient reinjured his left knee and was diagnosed with a patellar tendon rupture. The previously reconstructed ACL was intact. A posterior tibialis tendon graft was used to repair the patellar tendon via a transosseous tunnel in the tibial tuberosity. The patient’s recovery was complicated by a superficial wound that resolved with treatment. He achieved full range of motion and was able to return to sport. Conclusion: No technique for treating patellar tendon rupture following BPTB ACL reconstruction has been widely accepted. The treatment of this injury is left to the preference of the surgeon. This case demonstrates that tibialis posterior allografts are a viable option for the treatment of such injuries.
Stress-free cell aggregation by using the CEPT cocktail enhances embryoid body and organoid fitness

Embryoid bodies (EBs) and self-organizing organoids derived from human pluripotent stem cells (hPSCs) recapitulate tissue development in a dish and hold great promise for disease modeling and drug development. However, current protocols are hampered by cellular stress and apoptosis during cell aggregation, resulting in variability and impaired cell differentiation. Here, we demonstrate that EBs and various organoid models (e.g., brain, gut, kidney) can be optimized by using the small molecule cocktail named CEPT (chroman 1, emricasan, polyamines, trans-ISRIB), a polypharmacological approach that ensures cytoprotection and cell survival. Application of CEPT for just 24 h during cell aggregation has long-lasting consequences affecting morphogenesis, gene expression, cellular differentiation, and organoid function. Various qualification methods confirmed that CEPT treatment enhanced experimental reproducibility and consistently improved EB and organoid fitness as compared to the widely used ROCK inhibitor Y-27632. Collectively, we discovered that stress-free cell aggregation and superior cell survival in the presence of CEPT are critical quality control determinants that establish a robust foundation for bioengineering complex tissue and organ models.
Changes in serum and faecal zinc concentrations following supplementation with zinc sulphate heptahydrate of extensively grazed dairy cattle in New Zealand

ABSTRACT Aims To examine the relationship in dairy cattle between serum and faecal Zn concentrations and daily intake of Zn supplemented with an oral drench; and whether total daily intake (TDI) of Zn in dairy cattle can be predicted from single measurements of Zn concentration in serum or faeces. Methods A convenience sample of 20 animals from three stock classes (lactating cows, dry cows, heifers), that had not received Zn supplementation in the previous 60 days, was enrolled in the study. From Days −7 to −1, animals received no Zn supplementation. On Day 0, 15 animals per class were assigned daily drenching with increasing doses of ZnSO4.7H2O while five remained controls. From Days 0–6, treatment animals received 12.5 mg/kg LWT of Zn/day; from Days 7–13, 25 mg/kg LWT Zn/day and from Days 14–20, 37.5 mg/kg LWT Zn/day. Animals co-grazed within each stock class. Pasture, serum and faecal samples were collected at the start and at weekly intervals before each increase in Zn supplementation. Mixed and non-parametric models were used to assess treatment effects and whether daily intake of Zn could be predicted from Zn concentrations in serum and faeces. Results Dosing with 0, 12.5, 25.0 and 37.5 mg Zn/kg LWT resulted in serum Zn concentrations of 12.1, 16.7, 27.2 and 35.8 µmol/L in heifers, 13.3, 17.1, 26.4 and 40.0 µmol/L in dry and 11.9, 12.1, 23.4 and 27.2 µmol/L in lactating cows. Dosing with the same amounts of Zn resulted in faecal Zn concentrations of 2.95, 21.72, 40.32 and 53.27 mmol/kg DM in heifers, 2.81, 23.77, 55.16 and 68.20 mmol/kg DM in dry and 3.00, 12.71, 34.86 and 57.53 mmol/kg DM in lactating cows, respectively. Treatment elevated serum and faecal Zn concentrations above controls (p < 0.001). Supplemented lactating cows had lower serum Zn concentrations than dry cows or heifers (p < 0.01). Supplemented dry cows had faecal DM Zn concentrations higher than heifers or lactating cows (p < 0.05). Analysis showed serum and faecal Zn concentrations could predict TDI of Zn (p < 0.001). Concentrations of Zn in faeces estimated TDI of Zn within a narrower predictive interval than serum Zn concentrations. Conclusions and clinical relevance Concentrations of Zn in serum and faeces were positively associated with TDI of Zn in dairy cattle and could predict TDI of Zn. When using serum and faecal Zn concentrations to estimate TDI Zn, stock class must be accounted for.
Primary Care Patient Interest in Multi-Cancer Early Detection for Cancer Screening

Multi-cancer early detection (MCED) tests are being developed, but little is known about patient receptivity to their use for cancer screening. The current study assessed patient interest in such testing. Our team conducted a prospective, observational study among primary care patients in a large, urban health system. They were asked to complete a telephone survey that briefly described a new blood test in development to identify multiple types of cancer, but was not currently recommended or covered by insurance. The survey included items to assess respondent background characteristics, perceptions about MCED testing, and interest in having such an MCED test. We also used multivariable analyses to identify factors associated with patient interest in test use. In 2023, we surveyed 159 (32%) of 500 identified patients. Among respondents, 125 (79%) reported a high level of interest in having an MCED test. Interest was not associated with personal background characteristics, but was positively associated with the following expectations: testing would be recommended for cancer screening, be convenient, and be effective in finding early-stage disease (OR = 11.70, 95% CI: 4.02, 34.04, p < 0.001). Research is needed to assess patient interest and actual uptake when detailed information on testing is presented in routine care.
Utilizing random forests imputation of forest plot data for landscape-level wildfire analyses

Maps of the number, size, and species of trees in forests across the United States are desirable for a number of applications. For landscape-level fire and forest simulations that use the Forest Vegetation Simulator (FVS), a spatial tree-level dataset, or “tree list”, is a necessity. FVS is widely used at the stand level for simulating fire effects on tree mortality, carbon, and biomass, but uses at the landscape level are limited by lack of availability of forest inventory data for large contiguous areas. Detailed mapping of trees across large areas is not feasible with current technologies, but statistical methods for matching forest plot data with biophysical characteristics of the landscape offer a practical means to populate landscapes with a limited set of forest plot inventory data. We used a modified random forests approach, with Landfire vegetation and biophysical predictors at 30m grid resolution. In essence, the random forests method creates a “forest” of decision trees in order to choose the forest plot with the best statistical match for each grid cell in the landscape. Landfire data was used in this project because is publicly available, offers seamless coverage of variables needed for fire models, and is consistent with other datasets, including burn probabilities and flame length probabilities generated for the continental US by Fire Program Analysis (FPA). We used the imputed forest plot data to generate a map of forest cover and height as well as existing vegetation group for a study area in eastern Oregon, and examined correlations with Landfire data. The results showed good correspondence between the two data sets (84-97% within-class agreement, depending on the variable). In future research, the new imputed grid of inventory data will be used for landscape simulation studies to determine risk to terrestrial carbon resources from wildfire as well as to investigate the effect of fuel treatments on burn probability and fire sizes.
5. STRONTIUM-ISOTOPE STRATIGRAPHY OF LOWER CRETACEOUS ATOLL CARBONATES IN THE MID-PACIFIC MOUNTAINS1

Strontium-isotope ratios of Cretaceous shallow-water carbonates from two guyots in the Mid-Pacific Mountains are compared with high-resolution data derived from stratigraphically well-calibrated belemnites and oysters from sequences in England. The thickest section penetrated on Resolution Guyot can, with the aid of carbon-isotop e data, be divided into stages ranging from uppermost Hauterivian to the Albian/Cenomanian boundary. The section on Allison Guyot, although more ambiguous in interpretation, is exclusively Albian, and its upper limit is also close to the contact with the Albian/Cenomanian boundary. Comparison of age-vs.-thickness data on the two guyots suggests that Allison was subsiding at a rate at least twice that of Resolution Guyot during the Albian. The strontium-isotope data are compatible with the hypothesis of synchronous cessation of deposition of shallow-water carbonates at both sites.
Understanding the impact of the COVID-19 pandemic on U.S. older adults: self-reported pandemic-related concerns and consequences in a cross-sectional survey study

Background and objectives The purpose of this study was to explore COVID-19 pandemic-related concerns among a racially and ethnically representative sample of older adults in the U.S. Research design and methods Participants were 501 English-speaking adults 60 years and older recruited online nationally across the U.S. from Amazon Mechanical Turk (mTurk) and Prolific Research Platforms during June of 2020. Data comes from a larger cross-sectional survey. We content analyzed open-ended responses about pandemic-related concerns and observed responses to a checklist of items created by the research team to assess for specific physical, social, and financial consequences experienced due to the pandemic. Results A majority of the sample (92%) reported at least one pandemic-related concern, with the highest percentage expressing concerns coded as Concern for Others (28%), Physical Health (27%), Socializing (24%), Finance (15%) and Socio-Political-Economic (14%). Participants reported high concern severity (M = 4.03, SD = 1.04) about their concerns mentioned in response to the open-ended concerns question. When prompted with a checklist of items, participants frequently endorsed disruption in social activities as a consequence of the pandemic (83%), disruptions that could impact physical health (45%), and concern over finances as a consequence of the pandemic (41%). Discussion and implications Older adults most frequently mentioned concerns about the well-being and behavior of others, one’s own physical health, and the impacts of the pandemic and social distancing policies on social activities. Findings align with the Socioemotional Selectivity Theory and point to the importance of supporting older adults to maintain meaningful social engagement under conditions of a pandemic and social distancing policies.
The Region of Large Sea Surface Height Variability in the Southeast Pacific Ocean

Satellite altimeter observations of sea surface height (SSH) show an extensive triangular region of high variability in the southeastern Pacific. The region is unusual in two ways. First, it appears to have a horizontal correlation scale that is much larger than that associated with the mesoscale eddy-rich regions of the deep ocean. Second, the feature appears to reflect the shape of the underlying topography. Previous computer studies have suggested that it is a Rossby wave trapped by topography. Here detailed results are presented from a study that used a high-resolution global ocean model forced by 6-hourly ECMWF winds. The empirical orthogonal modes of the region are calculated, and it is shown that 29{percnt} of the SSH variance is due to a single mode with a similar shape to the region of high variability. The time series of the mode is correlated against the local Ekman pumping, and it is shown that the largest correlation is obtained when the lag is approximately 24 hours and the wind curl is averaged over a region roughly the size of the mode itself. The response function relating the amplitude of the mode time series to the amplitude of the forcing is calculated and is found to be dominated by a resonance at zero frequency and a decay time of 2.7 days. The results indicate that the feature is a highly damped geostrophic mode of the ocean