Upper atmospheric long-term trends could be examined in the ion temperatures ($T_i$) at the ionospheric F-region altitudes by the close coupling between neutrals and ions. We have analyzed the $T_i$ data sets of Arecibo Observatory (AO) incoherent scatter radar (18\textdegree20’N, 66\textdegree45’W) from 1985 to 2019, to examine the long-term trends of the ion temperature as a function of height from $\sim$140 km to $\sim$677 km. For this, the responses of $T_i$ to solar and geomagnetic activities have been taken into account as forcings of the $T_i$ behavior as well the annual and semi-annual oscillations. By removing the known forcing that govern the Ti behavior by the difference between the $T_i$ data and a climatological model, our results indicate that the upper atmosphere/ionosphere over Arecibo is cooling over the 35 years studied. Around 350 km, our findings also show that the rate of cooling over Arecibo is lower than previously reported for high latitudes, suggesting a latitudinal dependency. These cooling trends are believed to be the result of increasing green house gases, but the observed cooling trends exceed the magnitude of the cooling expected from green house gases. We have made an attempt to find the additional driver for observed cooling trends by linking the these upper atmospheric trends to lower atmospheric weather phenomena. We found that gravity waves in the lower atmosphere associated with terrestrial weather phenomena might be contributing to the observed cooling trends in the upper atmosphere.